http://www.rssboard.org/rss-specification 720 https://escholarship.org/uc/ucb_espm_org_oapdeposits/rss Recent eScholarship items from Division of Organisms & Environment Open Access Policy Deposits Thu, 27 Aug 2026 00:44:16 +0000 https://escholarship.org/uc/item/4v65j63k Wildlife is increasingly forced to share space with humans, facing disturbances that operate across different spatial and temporal scales. The press-pulse framework, originally developed in the disturbance ecology literature, distinguishes between long-term sustained 'presses' and more acute 'pulses'. Because pulses occur during ongoing press conditions, their ecological effects depend on how they interact with that background, helping explain why certain disturbances result in transient, localized changes, while others lead to lasting, widespread impacts. Here, we expand this framework by applying it to regimes of human disturbances, and incorporating 'pauses' as a third category. Pulses and pauses (e.g. episodes of extreme weather, or drastic changes in human mobility) can substantially affect wildlife behaviour, yet their effects are often modulated by background 'press' conditions. We offer a conceptual framework for disentangling effects across space and time and highlight... https://escholarship.org/uc/item/4v65j63k Wed, 26 Aug 2026 00:00:00 +0000 Ellis-Soto, Diego Abrahms, Briana Gaynor, Kaitlyn Rutz, Christian Schell, Christopher J https://orcid.org/0000-0002-2073-9852 https://escholarship.org/uc/item/94c6d3gt Under accelerating global change, trait-based approaches are emerging as essential tools in the ecological restoration toolbox. Where restoration has traditionally focused on the recovery of focal species in isolated systems, trait-based methods can provide a common language that extends beyond species- or system-specific contexts, allowing scientists and practitioners to translate insights across organisms and ecosystems and predict functional variation critical to resilience in the face of rapidly changing environmental conditions. Trait-based insights can thus help achieve restoration that is both adaptable and scalable as future climate scenarios unfold. To date, trait-based approaches to restoration have developed and proceeded independently across habitats and ecosystems, limiting information sharing and innovation. Here, we synthesize diverse perspectives and research on trait-informed restoration across ecosystems, distilling our findings into three key insights. First,... https://escholarship.org/uc/item/94c6d3gt Wed, 25 Mar 2026 00:00:00 +0000 Briand, Julia K Hosler, Sheryl C Merchant, Thomas K Vinebrooke, Rolf D Ostertag, Rebecca Symons, Celia C https://orcid.org/0000-0003-4120-0327 Cadotte, Marc W Eviner, Valerie T https://orcid.org/0000-0001-5530-9417 Bracken, Matthew ES https://orcid.org/0000-0002-0068-7485 Carlson, Rachel R Henn, Jonathan J Garbowski, Magda Bauer, Jonathan T Luong, Justin C https://orcid.org/0000-0003-2118-4788 Atkinson, Joe Hughes, A Randall Adams, Carrie Reinhardt Bates, Amanda E Funk, Jennifer L https://orcid.org/0000-0002-1916-5513 Love, Allegra E Zheng, Liting Galloway, Emily Green, Stephanie J https://escholarship.org/uc/item/6j29949v Abstract Biodiversity loss and unequal access to nature limit both ecological knowledge and opportunities for experiential learning. Here I present a portable, power outlet–independent educational toolkit that integrates AI‐assisted bird detection (Haikubox, BirdNET‐Pi, Merlin Bird ID) with off‐the‐shelf sound‐recording and music‐creation hardware using Ableton Move. This interdisciplinary approach engages participants in active listening, outdoor exploration, and place‐based music‐making using locally recorded bird vocalizations. Self‐reflection from two case studies in Connecticut and California, USA, suggests that this approach can (1) broaden participation in biodiversity monitoring, (2) help demystify AI and acoustic sensing technologies, (3) generate biodiversity observations, and (4) offer an accessible model for integrating music into environmental education. By linking environmental justice, ecological monitoring, biodiversity gap‐filling, and critical engagement with... https://escholarship.org/uc/item/6j29949v Wed, 25 Mar 2026 00:00:00 +0000 Ellis‐Soto, Diego https://escholarship.org/uc/item/2bq3438g Abstract Understanding the changes in crop yield stability ( μ /σ) under climate change is critical for food security and farmer livelihoods. Unstable crop yields have been identified as detrimental to international food trade and markets. However, the association between climate extremes and crop yield stability has not been well documented. Here, we present the sensitivity of corn and soybean yield stability to heat, drought and excessive wetness by using statistical modeling for rainfed corn and soybean based on survey yield records in the US Midwest. The results using survey data indicate that increased heat, drought and excessive wetness are collectively associated with reduced yield stability for corn and soybean. We find that the changes in corn and soybean yield stability in the US Midwest are predominantly related to heat stress. Additionally, irrigation can mitigate the yield stability reduction associated with heat and drought. In contrast, well‐irrigated yield is... https://escholarship.org/uc/item/2bq3438g Wed, 3 Dec 2025 00:00:00 +0000 Liu, Weihang Zhou, Junxiong https://orcid.org/0000-0001-7455-0759 Luo, Yuchuan Chen, Shuo Ma, Yuchi https://escholarship.org/uc/item/0vm6r158 Climate warming affects global livestock productivity. The meat yield from cattle farming (cattle meat per animal) represents livestock productivity at the individual level. However, the impact of warming on cattle meat yield at a global scale is not well understood. In this study, we combine country-level data on the annual meat yield from cattle farming and socioeconomic data from 1961 to 2020 with climate projections from General Circulation Models. The findings show that cattle meat yield increases as temperatures rise from low to medium and then decreases when annual average temperatures exceed 7 °C; this repose is pronounced in the grassland-based livestock system. Further, we show that warming creates unequal impacts between high- and low-income countries due to the divergent baseline temperature conditions. Future warming aggravates these unequal burdens between countries, with the most pronounced effects observed under the upper-middle emissions scenario. https://escholarship.org/uc/item/0vm6r158 Wed, 3 Dec 2025 00:00:00 +0000 Liu, Weihang Zhou, Junxiong https://orcid.org/0000-0001-7455-0759 Ma, Yuchi Chen, Shuo Luo, Yuchuan https://escholarship.org/uc/item/6c84d2h7 Body size is one of the most important traits governing individual-level demographic rates and modulating population-level processes. Multiple size-dependent demographic rates can simultaneously change population structure, so distinguishing their individual contributions to overall population dynamics remains a challenge. Disentangling size-dependent harvest rates from other demographic rates is critical for assessing the impact of removal on populations of invasive species. Inference about invasive populations can be difficult, however, as observations are often collected opportunistically as part of removal programs, rather than experimentally designed. Yet accurate inference is essential for understanding the feasibility of population suppression and optimising management decisions. We develop an integrated integral projection model (IPM²) that leverages the strengths of the integrated population model and integral projection model to enable inference about complex,... https://escholarship.org/uc/item/6c84d2h7 Wed, 19 Nov 2025 00:00:00 +0000 Keller, Abigail G https://orcid.org/0000-0001-6068-0173 Goldstein, Benjamin R Skare, Leah de Valpine, Perry https://orcid.org/0000-0002-8329-6796 https://escholarship.org/uc/item/98p3j120 Jumping in animals presents an interesting locomotory strategy as it requires the generation of large forces and accurate timing. Jumping in arachnids is further complicated by their semi-hydraulic locomotion system. Among arachnids, jumping spiders (Family Salticidae) are agile and dexterous jumpers. However, less is known about jumping in small salticid species. Here we used Habronattus conjunctus, a small jumping spider (body length ~ 4.5&nbsp;mm) to examine its jumping performance and compare it to that of other jumping spiders and insects. We also explored how legs are used during the takeoff phase of jumps. Jumps were staged between two raised platforms. We analyzed jumping videos with DeepLabCut to track 21 points on the cephalothorax, abdomen, and legs. By analyzing leg liftoff and extension patterns, we found evidence that H. conjunctus primarily uses the third legs to power jumps. We also found that H. conjunctus jumps achieve lower takeoff speeds and accelerations than... https://escholarship.org/uc/item/98p3j120 Wed, 22 Oct 2025 00:00:00 +0000 Brandt, Erin E Sasiharan, Yoshan Elias, Damian O https://orcid.org/0000-0002-5895-4275 Mhatre, Natasha https://escholarship.org/uc/item/6z555126 Understanding diversity has been a pursuit in evolutionary biology since its inception. A challenge arises when sexual selection has played a role in diversification. Questions of what constitutes a 'species', homoplasy vs. synapomorphy, and whether sexually selected traits show phylogenetic signal have hampered work on many systems. Peacock spiders are famous for sexually selected male courtship dances and peacock-like abdominal ornamentation. This lineage of jumping spiders currently includes over 90 species classified into two genera, Maratus and Saratus. Most Maratus species have been placed into groups based on secondary sexual characters, but evolutionary relationships remain unresolved. Here we assess relationships in peacock spiders using phylogenomic data (ultraconserved elements and RAD-sequencing). Analyses reveal that Maratus and the related genus Saitis are paraphyletic. Many, but not all, morphological groups within a 'core Maratus' clade are recovered as genetic... https://escholarship.org/uc/item/6z555126 Wed, 22 Oct 2025 00:00:00 +0000 Girard, Madeline B Elias, Damian O https://orcid.org/0000-0002-5895-4275 Azevedo, Guilherme Bi, Ke Kasumovic, Michael M Waldock, Julianne M Rosenblum, Erica Bree Hedin, Marshal https://escholarship.org/uc/item/6jp6d529 Environmental context is a crucial factor that influences sexual communication systems. Particularly in ectotherms, which cannot metabolically regulate their body temperature, temperature has an outsized effect on these intraspecific interactions. Using the desert-dwelling jumping spider Habronattus clypeatus, we assessed how temperature impacts various parts of the male signal and female mate choice for the signal. These spiders have multimodal, temporally structured courtship displays that begin with visual-only ‘sidling’ displays and proceed to multimodal visual and vibratory displays. To examine temperature effects, we performed sequential choice mating experiments (N =45 trials) at two temperature treatments: hot (∼50°C) and room temperature (∼25°C). We found first that variation in the different stages of courtship segregated onto different principal components. The only aspect of male courtship that females expressed preference for was sidling courtship, but only at the... https://escholarship.org/uc/item/6jp6d529 Wed, 22 Oct 2025 00:00:00 +0000 Brandt, Erin E Rosenthal, Malcolm F Elias, Damian O https://orcid.org/0000-0002-5895-4275 https://escholarship.org/uc/item/5dv5g42h Animal movements are highly constrained by morphology and energetics. In addition, predictable bodily damage can constrain locomotion even further. For example, for animals moving on land, losing legs may impose additional costs. We tested if losing legs affects the distance travelled over time (endurance) and the metabolic costs of locomotion (oxygen consumption) in Nelima paessleri harvestmen. These arachnids voluntary releases legs (i.e., autotomy) in response to predation attempts. We used flow-through respirometry as animals moved on a treadmill inside a sealed chamber. We found that endurance decreased gradually with an increasing number of legs lost. Interestingly, oxygen consumption increased only for harvestmen that lost three legs, but not for individuals that lost only a single leg. These results have different ecological and evolutionary implications. Reduced endurance may impair an animal’s ability to continue moving away from potential predators, while increased... https://escholarship.org/uc/item/5dv5g42h Wed, 22 Oct 2025 00:00:00 +0000 Escalante, Ignacio Ellis, Veronica R Elias, Damian O https://orcid.org/0000-0002-5895-4275 https://escholarship.org/uc/item/4tm7k9jc Because habitats present different costs and benefits in contexts ranging from foraging to mating to predator avoidance, decisions about habitat use likely involve significant trade-offs across behavioural contexts. We examine this possibility in Schizocosa floridana, a cursorial wolf spider whose habitat consists of multiple substrates, including oak and pine litter, and sand. However, S.&nbsp;floridana restricts its use of habitat to oak litter. Substrate environments vary significantly in the degree to which they transmit visual and vibratory information. Previous work found that oak litter best transmits the substrate-borne vibrations that are critical to mating communication. However, oak litter may reduce the availability of visual information, which is known to be important for prey capture in other wolf spider species. Here, we test the relationship between substrate and prey capture efficiency in S.&nbsp;floridana. We examine substrate use in a foraging context via two... https://escholarship.org/uc/item/4tm7k9jc Wed, 22 Oct 2025 00:00:00 +0000 Meza, Pablo Elias, Damian O https://orcid.org/0000-0002-5895-4275 Rosenthal, Malcolm F https://escholarship.org/uc/item/3219k9vh Abstract. It is not uncommon to find courtship displays that incorporate numerous components across different sensory modalities. We studied displays in male jumping spiders of the genus Habronattus F.O. Pickard-Cambridge, 1901, which court females using a combination of ornament and motion (dance) displays coordinated with vibrational songs. To explore the diversity in Habronattus courtship complexity, we focused on quantifying the dance and vibratory displays in nine members of the Habronattus clypeatus species group, with preliminary observations on two additional species from this group. Additionally, we looked at display variation across populations in two widespread species from this group. We document three main courtship types: "stilting", "buzzing", and "spinning", each identifiable by the presence or emphasis on particular display types. We found that for the widespread species H. clypeatus (Banks, 1895), different populations differed significantly and could be classified... https://escholarship.org/uc/item/3219k9vh Wed, 22 Oct 2025 00:00:00 +0000 Rivera, Christine Hedin, Marshal Mason, Andrew C Maddison, Wayne P Elias, Damian O https://orcid.org/0000-0002-5895-4275 https://escholarship.org/uc/item/25t0q5nc Nests are crucial to the survival of offspring and reproductive success of the animals that build them. These benefits are subject to change over time due to fluctuating conditions inside and outside of nests. For many species, nests are assumed to benefit offspring until they disperse and therefore, nest destruction prior to offspring dispersal results in reduced reproductive success for parents. However, the consequences of nest destruction to reproductive success, or lack thereof, remain largely unstudied across diverse taxa. Here, we experimentally investigate the function and benefits of nests of a mound-building spider. Mason spiders (Castianeira sp.) are wandering spiders that build intricate nests (mounds) on top of their egg sacs. Their offspring inhabit egg sacs at nest sites for up to 7&nbsp;months, including through winter. We find that despite requiring hundreds of collecting trips and many hours to construct, mason spider nests remain for a small portion of time... https://escholarship.org/uc/item/25t0q5nc Wed, 22 Oct 2025 00:00:00 +0000 Raboin, Maggie Elias, Damian O https://orcid.org/0000-0002-5895-4275 https://escholarship.org/uc/item/1x0207r4 Feathers can produce sound by fluttering in airflow. This flutter is hypothesized to be aeroelastic, arising from the coupling of aerodynamic forces to one or more of the feather's intrinsic structural resonance frequencies. We investigated how mode of flutter varied among a sample of hummingbird tail feathers tested in a wind tunnel. Feather vibration was measured directly at ~100 points across the surface of the feather with a scanning laser Doppler vibrometer (SLDV), as a function of airspeed, Uair. Most feathers exhibited multiple discrete modes of flutter, which we classified into types including tip, trailing vane and torsional modes. Vibratory behavior within a given mode was usually stable, but changes in independent variables such as airspeed or orientation sometimes caused feathers to abruptly 'jump' from one mode to another. We measured structural resonance frequencies and mode shapes directly by measuring the free response of 64 feathers stimulated with a shaker and... https://escholarship.org/uc/item/1x0207r4 Wed, 22 Oct 2025 00:00:00 +0000 Clark, Christopher J https://orcid.org/0000-0001-7943-9291 Elias, Damian O https://orcid.org/0000-0002-5895-4275 Girard, Madeline B Prum, Richard O https://escholarship.org/uc/item/15j8s616 Abstract: Defensive strategies, like other life-history traits favored by natural selection, may pose constraints on reproduction. A common anti-predator defense strategy that increases immediate survival is autotomy—the voluntary release of body parts. This type of morphological damage is considered to impose future costs for reproduction and fitness. We tested an alternative hypothesis that animals are robust (able to withstand and overcome perturbations) to this type of damage and do not experience any fitness costs in reproductive contexts. We explored the effects of experimental leg loss on the reproductive behavior of one species of Neotropical Prionostemma harvestmen. These arachnids undergo autotomy frequently, do not regenerate legs, and their courtship and mating necessitate the use of legs. We assessed the effect of losing different types of legs (locomotor or sensory) on courtship behavior and mating success in males. We found no differences in the mating success or... https://escholarship.org/uc/item/15j8s616 Wed, 22 Oct 2025 00:00:00 +0000 Escalante, Ignacio Elias, Damian O https://orcid.org/0000-0002-5895-4275 https://escholarship.org/uc/item/14x6m472 In animal taxa, the behavior of choosing a microhabitat determines the context in which individuals engage in all other behaviors and interactions. Microhabitat choice has particularly important implications for animal communication, because the successful transmission of information between individuals is highly context-dependent. Substrate-borne vibrations, which are commonly produced, detected, and used for communication by arthropods, are especially influenced by substrate choice because substrates vary widely in their vibration transmission properties. In this laboratory-based study, we examine vibration transmission properties of substrates commonly encountered in nature by the jumping spider Habronattus clypeatus and also examine whether these spiders exhibit a preference for particular substrates using a choice experiment. We predicted that spiders would prefer substrates that can better transmit vibratory signals. We found that leaf litter minimized the attenuation of... https://escholarship.org/uc/item/14x6m472 Wed, 22 Oct 2025 00:00:00 +0000 Sun, Yuheng Brandt, Erin E Elias, Damian O https://orcid.org/0000-0002-5895-4275 Rosenthal, Malcolm Kamath, Ambika https://escholarship.org/uc/item/13q0f7m9 Animals communicate using a diversity of signals produced by a wide array of physical structures. Determining how a signal is produced provides key insights into signal evolution. Here, we examine a complex vibratory mating display produced by male Schizocosa floridana wolf spiders. This display contains three discrete substrate-borne acoustic components (known as “thumps”, “taps”, and “chirps”), each of which is anecdotally associated with the movement of a different body part (the pedipalps, legs, and abdomen respectively). In order to determine the method of production, we employ a combination of high-speed video/audio recordings and SEM imaging of possible sound-producing structures. Previous work has suggested that the “chirp” component is tonal, a signal trait that would be potentially unique in the genus. We measured signal tonality for all courtship components, as well as for courtship components from sixteen other Schizocosa wolf spiders. Our results suggest that S. floridana... https://escholarship.org/uc/item/13q0f7m9 Wed, 22 Oct 2025 00:00:00 +0000 Rosenthal, Malcolm F Hebets, Eileen A McGinley, Rowan Raiza, Cody Starrett, James Yan, Lin Elias, Damian O https://orcid.org/0000-0002-5895-4275 https://escholarship.org/uc/item/86r9r77f 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... https://escholarship.org/uc/item/86r9r77f Thu, 2 Oct 2025 00:00:00 +0000 Stemkovski, Michael Bernhardt, Joey R Blonder, Benjamin Wong https://orcid.org/0000-0002-5061-2385 Bradford, John B Clark‐Wolf, Kyra Dee, Laura E Evans, Margaret EK Iglesias, Virginia Johnson, Loretta C Lynch, Abigail J Malone, Sparkle L Osborne, Brooke B Pastore, Melissa A Paterson, Michael Pinsky, Malin L https://orcid.org/0000-0002-8523-8952 Rollinson, Christine R Selmoni, Oliver Venkiteswaran, Jason J Walker, Anthony P Ward, Nicole K Williams, John W Zarakas, Claire M Adler, Peter B https://escholarship.org/uc/item/7bv1m6gp Spurred by nationwide protests against anti-Black violence in the summer of 2020, academic departments across the USA saw an uptick in efforts to integrate belonging, diversity, equity, justice, and inclusion initiatives into their programs. In this vein, graduate students in the Department of Environmental Science, Policy, and Management at the University of California, Berkeley, developed and led a semester-long course, “Critical Engagements in Anti-Racist Environmental Scholarship.” The course cultivated anti-racist mindsets through collaborative learning and action projects. We designed and taught the class as a team of doctoral students, and course participants consisted of faculty, staff, postdoctoral scholars, and other graduate students, thus disrupting traditional academic power structures. In this article, we draw on our experiences from two years of developing and teaching this course. We begin by outlining our theory of change, depicted as a tree rooted in our pedagogical... https://escholarship.org/uc/item/7bv1m6gp Wed, 10 Sep 2025 00:00:00 +0000 Mgbara, Whitney Fanshel, Rosalie Zdzienicka Esquivel, Kenzo Shannon, Natasha Parker-Shames, Phoebe Elias, Damian O https://orcid.org/0000-0002-5895-4275 Washington, Lorenzo https://orcid.org/0000-0002-0624-4693 Guzman, Aidee https://escholarship.org/uc/item/66j8w0h4 Heterospecific interactions between nascent species offer insights into how sexual selection shapes novel traits, illuminating patterns in species interactions and diversification. We tested female preferences between two recently diverged, allopatric species of jumping spiders: <i>Habronattus americanus</i> PLC, with red-coloured males performing short multimodal displays, and <i>Habronattus sansoni</i> CC, with brown-coloured males performing long multimodal displays. Mate choice experiments showed that females of both species preferred <i>H. americanus</i> PLC males. To examine the role of red coloration, we manipulated male coloration in both species. Results indicated that red-painted <i>H. sansoni</i> CC males experienced an increase in mating success, whereas brown-painted <i>H. americanus</i> PLCmales did not show reduced success. Our study suggests that (i) strong latent female preferences can drive unidirectional introgression across species boundaries, potentially leading... https://escholarship.org/uc/item/66j8w0h4 Wed, 10 Sep 2025 00:00:00 +0000 Yan, Lin Huh, Noah Joon Ibañez, Daniel Rosenthal, Malcolm F Hedin, Marshal Elias, Damian O https://orcid.org/0000-0002-5895-4275 https://escholarship.org/uc/item/2v43h64m The selection of animal signal form often changes significantly with the environment, yet signal form may be environment-dependent. Little is known about how variation in individual responses to changing environments affects the relationship between selection and the subsequent evolution of signal traits. To address this question, we assess the effects of variation in temperature on individual signaling and mating behavior responses across temperatures in the wolf spider Schizocosa floridana. By running repeated-measures trials, we find that temperature has predictable effects on signal form, but that the performance of individual courters is not consistent across temperatures. Traits associated with courtship rate generally increase at higher temperatures but inter-individual consistency in response to temperature change is low, despite consistent female preferences for increased courtship rate at all temperatures. Interestingly, the production of the likely most recently evolved... https://escholarship.org/uc/item/2v43h64m Wed, 10 Sep 2025 00:00:00 +0000 Rosenthal, Malcolm F Elias, Damian O https://orcid.org/0000-0002-5895-4275 https://escholarship.org/uc/item/9zf7k90g Microclimate, an important part of ecology and biogeography https://escholarship.org/uc/item/9zf7k90g Fri, 29 Aug 2025 00:00:00 +0000 Kemppinen, Julia Lembrechts, Jonas J Van Meerbeek, Koenraad Carnicer, Jofre Chardon, Nathalie Isabelle Kardol, Paul Lenoir, Jonathan Liu, Daijun Maclean, Ilya Pergl, Jan Saccone, Patrick Senior, Rebecca A Shen, Ting Słowińska, Sandra Vandvik, Vigdis von Oppen, Jonathan Aalto, Juha Ayalew, Biruk Bates, Olivia Bertelsmeier, Cleo Bertrand, Romain Beugnon, Rémy Borderieux, Jeremy Brůna, Josef Buckley, Lauren Bujan, Jelena Casanova‐Katny, Angelica Christiansen, Ditte Marie Collart, Flavien De Lombaerde, Emiel De Pauw, Karen Depauw, Leen Di Musciano, Michele Borrego, Raquel Díaz Díaz‐Calafat, Joan Ellis‐Soto, Diego Esteban, Raquel de Jong, Geerte Fälthammar Gallois, Elise Garcia, Maria Begoña Gillerot, Loïc Greiser, Caroline Gril, Eva Haesen, Stef Hampe, Arndt Hedwall, Per‐Ola Hes, Gabriel Hespanhol, Helena Hoffrén, Raúl Hylander, Kristoffer Jiménez‐Alfaro, Borja Jucker, Tommaso Klinges, David Kolstela, Joonas Kopecký, Martin Kovács, Bence Maeda, Eduardo Eiji Máliš, František Man, Matěj Mathiak, Corrie Meineri, Eric Naujokaitis‐Lewis, Ilona Nijs, Ivan Normand, Signe Nuñez, Martin Orczewska, Anna Peña‐Aguilera, Pablo Pincebourde, Sylvain Plichta, Roman Quick, Susan Renault, David Ricci, Lorenzo Rissanen, Tuuli Segura‐Hernández, Laura Selvi, Federico Serra‐Diaz, Josep M Soifer, Lydia Spicher, Fabien Svenning, Jens‐Christian Tamian, Anouch Thomaes, Arno Thoonen, Marijke Trew, Brittany Van de Vondel, Stijn van den Brink, Liesbeth Vangansbeke, Pieter Verdonck, Sanne Vitkova, Michaela Vives‐Ingla, Maria von Schmalensee, Loke Wang, Runxi Wild, Jan Williamson, Joseph Zellweger, Florian Zhou, Xiaqu Zuza, Emmanuel Junior De Frenne, Pieter https://escholarship.org/uc/item/6142t8bq Abstract: Over the past five decades, a large number of wild animals have been individually identified by various observation systems and/or temporary tracking methods, providing unparalleled insights into their lives over both time and space. However, so far there is no comprehensive record of uniquely individually identified animals nor where their data and metadata are stored, for example photos, physiological and genetic samples, disease screens, information on social relationships. Databases currently do not offer unique identifiers for living, individual wild animals, similar to the permanent ID labelling for deceased museum specimens. To address this problem, we introduce two new concepts: (1) a globally unique animal ID (UAID) available to define uniquely and individually identified animals archived in any database, including metadata archived at the time of publication; and (2) the digital ‘home’ for UAIDs, the Movebank Life History Museum (MoMu), storing and... https://escholarship.org/uc/item/6142t8bq Fri, 29 Aug 2025 00:00:00 +0000 Wikelski, Martin Quetting, Michael Bates, John Berger‐Wolf, Tanya Bohrer, Gil Börger, Luca Chapple, Taylor Crofoot, Margaret C Davidson, Sarah C Dechmann, Dina KN Ellis‐Soto, Diego Ellwood, Elizabeth R Fiedler, Wolfgang Flack, Andrea Fruth, Barbara Franconi, Novella Havmøller, Rasmus Worsøe Hirt, Julian Hussey, Nigel E Iannarilli, Fabiola Landwehr, Matthias Müller, Maximilian E Mueller, Thomas Mueller, Uschi Oliver, Ruth Y Partecke, Jesko Pokrovsky, Ivan Pokrovskaya, Liya Rubenstein, Dustin R Rutz, Christian Safi, Kamran Santangeli, Andrea van Schalkwyk, O Louis Sequeira, Ana MM Sherub, Sherub Ramesh, Tharmalingam Viljoen, Pauli Wasik, Kaja A Wild, Timm A Yanco, Scott Kays, Roland https://escholarship.org/uc/item/0px932d7 Hierarchical statistical models are important in applied sciences because they capture complex relationships in data, especially when variables are related by space, time, sampling unit, or other shared features. Existing methods for maximum likelihood estimation that rely on Monte Carlo integration over latent variables, such as Monte Carlo Expectation Maximization (MCEM), suffer from drawbacks in efficiency and/or generality. We harness a connection between sampling-stepping iterations for such methods and stochastic gradient descent methods for non-hierarchical models: many noisier steps can do better than few cleaner steps. We call the resulting methods Hierarchical Model Stochastic Gradient Descent (HMSGD) and show that combining efficient, adaptive step-size algorithms with HMSGD yields efficiency gains. We introduce a one-dimensional sampling-based greedy line search for step-size determination. We implement these methods and conduct numerical experiments for a Gamma-Poisson... https://escholarship.org/uc/item/0px932d7 Sat, 12 Apr 2025 00:00:00 +0000 Hong, Johnny Stoudt, Sara de Valpine, Perry https://orcid.org/0000-0002-8329-6796 https://escholarship.org/uc/item/1cj3j06s <p>Premise</p><p>Environmental DNA (eDNA) can be used to determine the composition of the soil biome community, revealing beneficial and antagonistic microbes and invertebrates associated with plants. eDNA analyses can complement traditional soil community studies, offering more comprehensive information for conservation practitioners. Studies are also needed to examine differences between field and greenhouse soil biomes because greenhouse-grown plants are often transplanted in the field during restoration efforts.</p><p>Methods</p><p>We used eDNA multilocus metabarcoding to test how the soil biome of the federally and state-endangered species,&nbsp;Lupinus nipomensis, differed between wet-cool and dry-warm microhabitats. At Arroyo Grande, California, 20 experimental plots were sampled, representing a factorial combination of wet-cool vs. dry-warm soil and plots that did or did not contain&nbsp;L. nipomensis. In a simultaneous greenhouse study,&nbsp;L. nipomensis&nbsp;was grown... https://escholarship.org/uc/item/1cj3j06s Wed, 9 Apr 2025 00:00:00 +0000 Nguyen, Peter T Luong, Justin C Wishingrad, Van Stratton, Lisa Loik, Michael E Meyer, Rachel S https://escholarship.org/uc/item/54d949hw The reintroduction of endangered plant species is an essential conservation tool. Reintroductions can fail to create resilient, self-sustaining populations due to a poor understanding of environmental factors that limit or promote plant success. Biotic factors, specifically plant-arthropod interactions, have been shown to affect the establishment of endangered plant populations. <i>Lupinus nipomensis</i> (Nipomo Mesa lupine) is a state of California (California Rare Plant Rank: 1B.1) and federally (65 FR 14888) endangered endemic plant with only one extant population located along the central California coast. How arthropods positively or negatively interact with <i>L</i>. <i>nipomensis</i> is not well known and more information could aid conservation efforts. We conducted arthropod surveys of the entire <i>L</i>. <i>nipomensis</i> extant population in spring 2017. Observed arthropods present on <i>L</i>.&nbsp;<i>nipomensis</i> included 17 families, with a majority of individuals... https://escholarship.org/uc/item/54d949hw Wed, 19 Mar 2025 00:00:00 +0000 Motta, Carina I Luong, Justin C https://orcid.org/0000-0003-2118-4788 Seltmann, Katja C https://orcid.org/0000-0001-5354-6048 https://escholarship.org/uc/item/3t47p11n It remains unclear to what extent shifts in gender attitudes are products of changes in micro-level characteristics, macro-level social transformations, or net cohort and period transitions. We test these questions on 20 waves of data from the General Social Survey, 1977-2016 (N = 45,125). Compositional change in individual characteristics accounts for almost 78 percent of the cohort variation in gender attitudes, but only 32 percent of the historical transformations. Macro dynamics are responsible for an additional 60 percent of the historical change in gender attitudes. Two structural forces are associated with historical transitions in American gender attitudes: gender equality in the labor force and the rise of men's overwork. Each of these factors accounts for a significant proportion of the period variation in gender attitudes in our analysis, and the rise of men's overwork appears to account for the puzzle of the "stalled revolution" in the 1990s and its "restart" in the... https://escholarship.org/uc/item/3t47p11n Tue, 25 Feb 2025 00:00:00 +0000 Shu, Xiaoling Meagher, Kelsey D https://escholarship.org/uc/item/461399nz In ecological and conservation studies, responsible researchers strive to obtain rich data while minimizing disturbance to wildlife and ecosystems. We assessed if samples collected noninvasively can be used for faecal microbiome research, comparing microbiota of noninvasively collected faecal samples to those collected from trapped common cranes at the same sites over the same periods. We found significant differences in faecal microbial composition (alpha and beta diversity), which likely did not result from noninvasive sample exposure to soil contaminants, as assessed by comparing bacterial oxygen use profiles. Differences might result from trapped birds' exposure to sedatives or stress. We conclude that if all samples are collected in the same manner, comparative analyses are valid, and noninvasive sampling may better represent host faecal microbiota because there are no trapping effects. Experiments with fresh and delayed sample collection can elucidate effects of environmental... https://escholarship.org/uc/item/461399nz Fri, 24 Jan 2025 00:00:00 +0000 Turjeman, Sondra Pekarsky, Sasha Corl, Ammon https://orcid.org/0000-0002-5156-4047 Kamath, Pauline L Getz, Wayne M https://orcid.org/0000-0001-8784-9354 Bowie, Rauri CK https://orcid.org/0000-0001-8328-6021 Markin, Yuri Nathan, Ran https://escholarship.org/uc/item/8h47p1xk Thermal soaring conditions above the sea have long been assumed absent or too weak for terrestrial migrating birds, forcing obligate soarers to take long detours and avoid sea-crossing, and facultative soarers to cross exclusively by costly flapping flight. Thus, while atmospheric convection does develop at sea and is used by some seabirds, it has been largely ignored in avian migration research. Here, we provide direct evidence for routine thermal soaring over open sea in the common crane, the heaviest facultative soarer known among terrestrial migrating birds. Using high-resolution biologging from 44 cranes tracked across their transcontinental migration over 4 years, we show that soaring performance was no different over sea than over land in mid-latitudes. Sea-soaring occurred predominantly in autumn when large water-air temperature difference followed mid-latitude cyclones. Our findings challenge a fundamental migration research paradigm and suggest that obligate soarers... https://escholarship.org/uc/item/8h47p1xk Tue, 21 Jan 2025 00:00:00 +0000 Pekarsky, Sasha Shohami, David Horvitz, Nir Bowie, Rauri CK https://orcid.org/0000-0001-8328-6021 Kamath, Pauline L Markin, Yuri Getz, Wayne M https://orcid.org/0000-0001-8784-9354 Nathan, Ran https://escholarship.org/uc/item/8850z243 Climate change is shifting the timing of organismal life-history events. Although consequential food-web mismatches can emerge if predators and prey shift at different rates, research on phenological shifts has traditionally focused on single trophic levels. Here, we analysed &gt;2000 long-term, monthly time series of phytoplankton, zooplankton, and fish abundance or biomass for the San Francisco, Chesapeake, and Massachusetts bays. Phenological shifts occurred in over a quarter (28%) of the combined series across all three estuaries. However, phenological trends for many taxa (ca. 29-68%) did not track the changing environment. While planktonic taxa largely advanced their phenologies, fishes displayed broad patterns of both advanced and delayed timing of peak abundance. Overall, these divergent patterns illustrate the potential for climate-driven trophic mismatches. Our results suggest that even if signatures of global climate change differ locally, widespread phenological change... https://escholarship.org/uc/item/8850z243 Fri, 17 Jan 2025 00:00:00 +0000 Fournier, Robert J Colombano, Denise D Latour, Robert J Carlson, Stephanie M https://orcid.org/0000-0003-3055-6483 Ruhi, Albert https://orcid.org/0000-0003-4011-6457 https://escholarship.org/uc/item/93q075bw The diversity of signalling traits within and across taxa is vast and striking, prompting us to consider how novelty evolves in the context of animal communication. Sexual selection contributes to diversification, and here we endeavour to understand the initial conditions that facilitate the maintenance or elimination of new sexual signals and receiver features. New sender and receiver variants can occur through mutation, plasticity, hybridization and cultural innovation, and the initial conditions of the sender, the receiver and the environment then dictate whether a novel cue becomes a signal. New features may arise in the sender, the receiver or both simultaneously. We contend that it may be easier than assumed to evolve new sexual signals because sexual signals may be arbitrary, sexual conflict is common and receivers are capable of perceiving much more of the world than just existing sexual signals. Additionally, changes in the signalling environment can approximate both... https://escholarship.org/uc/item/93q075bw Thu, 16 Jan 2025 00:00:00 +0000 Broder, E Dale Elias, Damian O https://orcid.org/0000-0002-5895-4275 Rodríguez, Rafael L Rosenthal, Gil G Seymoure, Brett M Tinghitella, Robin M https://escholarship.org/uc/item/85s190t7 To capture prey otherwise unattainable by muscle function alone, some animal lineages have evolved movements that are driven by stored elastic energy, producing movements of remarkable speed and force. One such example that has evolved multiple times is a trap-jaw mechanism, in which the mouthparts of an animal are loaded with energy as they open to a wide gape and then, when triggered to close, produce a terrific force. Within the spiders (Araneae), this type of attack has thus far solely been documented in the palpimanoid family Mecysmaucheniidae but a similar morphology has also been observed in the distantly related araneoid subfamily Pararchaeinae, leading to speculation of a trap-jaw attack in that lineage as well. Here, using high-speed videography, we test whether cheliceral strike power output suggests elastic-driven movements in the pararchaeine <i>Pararchaea alba</i>. The strike speed attained places <i>P. alba</i> as a moderately fast striker exceeding the slowest... https://escholarship.org/uc/item/85s190t7 Thu, 16 Jan 2025 00:00:00 +0000 Kallal, Robert J Elias, Damian O https://orcid.org/0000-0002-5895-4275 Wood, Hannah M https://escholarship.org/uc/item/3ck7p7cc Finding shelter and surviving encounters with predators are pervasive challenges for animals. These challenges may be exacerbated after individuals experience bodily damage. Certain forms of damage arise voluntarily in animals; for instance, some taxa release appendages (tails, legs, or other body parts) as a defensive strategy ("autotomy"). This behavior, however, may pose long-term negative consequences for habitat use and survival. Additionally, these putative consequences are expected to vary according to the function of the lost body part. We tested the effects of losing different functional leg types (locomotor or sensory) on future habitat use and survival in a Neotropical species of <i>Prionostemma</i> harvestmen (Arachnida: Opiliones) that undergo frequent autotomy but do not regrow limbs. Daytime surveys revealed that both eight-legged harvestmen and harvestmen missing legs roosted in similar frequencies across habitats (tree bark, mossy tree, or fern), and perched at... https://escholarship.org/uc/item/3ck7p7cc Thu, 16 Jan 2025 00:00:00 +0000 Escalante, Ignacio Elias, Damian O https://orcid.org/0000-0002-5895-4275 https://escholarship.org/uc/item/9xg35641 Sexual selection is an important evolutionary force and despite extensive research, understanding mate choice on naturally occurring trait variation remains an intriguing area of study. The correlation between mass, a trait associated with courter viability and common target for mate choice, and signals is particularly noteworthy. This study focuses on Schizocosa mccooki, the largest member of a wolf spider genus renowned for its diverse complex male courtship. Our objective was to understand the relationship of male mass and other courtship signals on female choice within this species. We conducted lab experiments involving random pairings of field caught males and females, recording vibratory courtship and its outcomes. Our findings revealed that S. mccooki courtship consisted of vibratory signals with two major components, thumps and raps. Male mass, overall courtship vigor, and thump duration were found to predict mating success. Interestingly, we found no correlation between... https://escholarship.org/uc/item/9xg35641 Wed, 15 Jan 2025 00:00:00 +0000 Yan, Lin Sabaria, Athena Elias, Damian O Rosenthal, Malcolm F https://escholarship.org/uc/item/62f2f66j Substrate-borne vibrations are ubiquitous in nature and are used by diverse taxa to communicate and to obtain information about their environments. However, substrate-borne vibrations remain understudied compared with other sensory and signaling modalities, in part due to human sensory biases. In addition, understanding and quantifying the transmission of vibrations remains a challenging task due to it being dependent on both signal properties and properties of the substrates that the signals transmit through. Here, we provide methods for playing back and measuring the transmission of vibrations throughout a substrate. Using linear resonant actuators, we conducted playbacks of pure tones and frequency sweeps on wooden dowels and on the stems of potted Ptelea trifoliata L. (Rutaceae) plants. We used scanning laser Doppler vibrometry to measure the signals at multiple locations along the length of the dowels and plant stems. We demonstrate that playback of a frequency sweep yields... https://escholarship.org/uc/item/62f2f66j Wed, 15 Jan 2025 00:00:00 +0000 McGinley, Rowan H Cocroft, Reginald B Elias, Damian O Redle, Elizabeth Gorlewicz, Jenna Fowler‐Finn, Kasey D https://escholarship.org/uc/item/6mt3j4k7 Indigenous peoples have cultivated biodiverse agroecosystems since time immemorial. The rise of metagenomics and high-throughput sequencing technologies in biodiversity studies has rapidly expanded the scale of data collection from these lands. A respectful approach to the data life cycle grounded in the sovereignty of indigenous communities is imperative to not perpetuate harm. In this paper, we operationalize an indigenous data sovereignty (IDS) framework to outline realistic considerations for genomic data that span data collection, governance, and communication. As a case study for this framework, we use arthropod genomic data collected from diversified and simplified farm sites close to and far from natural habitats within a historic Kānaka 'Ōiwi (Indigenous Hawaiian) agroecosystem. Diversified sites had the highest Operational Taxonomic Unit (OTU) richness for native and introduced arthropods. There may be a significant spillover effect between forest and farm sites, as... https://escholarship.org/uc/item/6mt3j4k7 Tue, 14 Jan 2025 00:00:00 +0000 Hutchins, Leke Mc Cartney, Ann Graham, Natalie Gillespie, Rosemary https://orcid.org/0000-0003-0086-7424 Guzman, Aidee https://escholarship.org/uc/item/7xb3t1m8 BackgroundSpecies host diverse microbial communities that can impact their digestion and health, which has led to much interest in understanding the factors that influence their microbiota. We studied the developmental, environmental, and social factors that influence the microbiota of nestling barn owls (Tyto alba) through a partial cross-fostering experiment that manipulated the social and nest environment of the nestlings. We then examined the nestling microbiota before and three weeks after the exchange of nestlings between nests, along with the microbiota of the adults at the nest and nestlings in unmanipulated nests.ResultsWe found that nestlings had higher bacterial diversity and different bacterial communities than adults. The microbiota of nestlings was more like that of their mothers than their fathers, but the similarity to the father tended to increase with the amount of time the father was in close proximity to the nest, as measured from movement data. Cross-fostered... https://escholarship.org/uc/item/7xb3t1m8 Mon, 6 Jan 2025 00:00:00 +0000 Corl, Ammon https://orcid.org/0000-0002-5156-4047 Charter, Motti Rozman, Gabe Turjeman, Sondra Toledo, Sivan Kamath, Pauline L Getz, Wayne M https://orcid.org/0000-0001-8784-9354 Nathan, Ran Bowie, Rauri CK https://orcid.org/0000-0001-8328-6021 https://escholarship.org/uc/item/48z6q134 Increasing heatwaves are threatening forest ecosystems globally. Leaf thermal regulation and tolerance are important for plant survival during heatwaves, though the interaction between these processes and water availability is unclear. Genotypes of the widely distributed foundation tree species <i>Populus fremontii</i> were studied in a controlled common garden during a record summer heatwave-where air temperature exceeded 48 °C. When water was not limiting, all genotypes cooled leaves 2 to 5 °C below air temperatures. Homeothermic cooling was disrupted for weeks following a 72-h reduction in soil water, resulting in leaf temperatures rising 3 °C above air temperature and 1.3 °C above leaf thresholds for physiological damage, despite the water stress having little effect on leaf water potentials. Tradeoffs between leaf thermal safety and hydraulic safety emerged but, regardless of water use strategy, all genotypes experienced significant leaf mortality following water stress.... https://escholarship.org/uc/item/48z6q134 Sat, 9 Nov 2024 00:00:00 +0000 Posch, Bradley C https://orcid.org/0000-0003-0924-6608 Bush, Susan E Koepke, Dan F Schuessler, Alexandra Anderegg, Leander LD Aparecido, Luiza MT Blonder, Benjamin W https://orcid.org/0000-0002-5061-2385 Guo, Jessica S Kerr, Kelly L Moran, Madeline E Cooper, Hillary F Doughty, Christopher E Gehring, Catherine A Whitham, Thomas G Allan, Gerard J Hultine, Kevin R https://escholarship.org/uc/item/0hm3v8zz Many terrestrial plant communities, especially forests, have been shown to lag in response to rapid climate change. Grassland communities may respond more quickly to novel climates, as they consist mostly of short-lived species, which are directly exposed to macroclimate change. Here we report the rapid response of grassland communities to climate change in the California Floristic Province. We estimated 349 vascular plant species’ climatic niches from 829,337 occurrence records, compiled 15 long-term community composition datasets from 12 observational studies and 3 global change experiments, and analysed community compositional shifts in the climate niche space. We show that communities experienced significant shifts towards species associated with warmer and drier locations at rates of 0.0216 ± 0.00592 °C yr−1 (mean ± s.e.) and −3.04 ± 0.742 mm yr−1, and these changes occurred at a pace similar to that of climate warming and drying. These directional shifts were consistent... https://escholarship.org/uc/item/0hm3v8zz Thu, 7 Nov 2024 00:00:00 +0000 Zhu, Kai Song, Yiluan Lesage, Josephine C Luong, Justin C https://orcid.org/0000-0003-2118-4788 Bartolome, James W Chiariello, Nona R Dudney, Joan Field, Christopher B Hallett, Lauren M Hammond, Michele Harrison, Susan P https://orcid.org/0000-0001-6278-2181 Hayes, Grey F Hobbs, Richard J Holl, Karen D https://orcid.org/0000-0003-2893-6161 Hopkinson, Peter Larios, Loralee https://orcid.org/0000-0002-9740-8111 Loik, Michael E https://orcid.org/0000-0003-0847-6778 Prugh, Laura R https://escholarship.org/uc/item/9bw656vf Animal movement plays a key role in many ecological processes and has a direct influence on an individual’s fitness at several scales of analysis (i.e., next-step, subdiel, day-by-day, seasonal). This highlights the need to dissect movement behavior at different spatio-temporal scales and develop hierarchical movement tools for generating realistic tracks to supplement existing single-temporal-scale simulators. In reality, animal movement paths are a concatenation of fundamental movement elements (FuMEs: e.g., a step or wing flap), but these are not generally extractable from a relocation time-series track (e.g., sequential GPS fixes) from which step-length (SL, aka velocity) and turning-angle (TA) time series can be extracted. For short, fixed-length segments of track, we generate their SL and TA statistics (e.g., means, standard deviations, correlations) to obtain segment-specific vectors that can be cluster into different types. We use the centroids of these clusters to obtain... https://escholarship.org/uc/item/9bw656vf Tue, 5 Nov 2024 00:00:00 +0000 Getz, Wayne M https://orcid.org/0000-0001-8784-9354 Salter, Richard Sethi, Varun Cain, Shlomo Spiegel, Orr Toledo, Sivan https://escholarship.org/uc/item/53h4r3m0 Polyergus kidnapper ants are widely distributed, but relatively uncommon, throughout the Holarctic, spanning an elevational range from sea level to over 3,000 m. These species are well known for their obligate social parasitism with various Formica ant species, which they kidnap in dramatic, highly coordinated raids. Kidnapped Formica larvae and pupae become integrated into the Polyergus colony where they develop into adults and perform nearly all of the necessary colony tasks for the benefit of their captors. In California, Polyergus mexicanus is the most widely distributed Polyergus, but recent evidence has identified substantial genetic polymorphism within this species, including genetically divergent lineages associated with the use of different Formica host species. Given its unique behavior and genetic diversity, P. mexicanus plays a critical role in maintaining ecosystem balance by influencing the population dynamics and genetic diversity of its host ant species, Formica,... https://escholarship.org/uc/item/53h4r3m0 Tue, 5 Nov 2024 00:00:00 +0000 Cash, Elizabeth I https://orcid.org/0000-0002-1192-3770 Escalona, Merly https://orcid.org/0000-0003-0213-4777 Ward, Philip S https://orcid.org/0000-0002-9019-0383 Sahasrabudhe, Ruta Miller, Courtney Toffelmier, Erin https://orcid.org/0000-0001-6028-8497 Fairbairn, Colin Seligmann, William https://orcid.org/0000-0002-5762-3095 Shaffer, H Bradley Tsutsui, Neil D https://escholarship.org/uc/item/9zj614c6 Concern for megafauna is increasing among scientists and non-scientists. Many studies have emphasized that megafauna play prominent ecological roles and provide important ecosystem services to humanity. But, what precisely are 'megafauna'? Here, we critically assess the concept of megafauna and propose a goal-oriented framework for megafaunal research. First, we review definitions of megafauna and analyse associated terminology in the scientific literature. Second, we conduct a survey among ecologists and palaeontologists to assess the species traits used to identify and define megafauna. Our review indicates that definitions are highly dependent on the study ecosystem and research question, and primarily rely on <i>ad hoc</i> size-related criteria. Our survey suggests that body size is crucial, but not necessarily sufficient, for addressing the different applications of the term megafauna. Thus, after discussing the pros and cons of existing definitions, we propose an additional... https://escholarship.org/uc/item/9zj614c6 Sun, 18 Aug 2024 00:00:00 +0000 Moleón, Marcos Sánchez-Zapata, José A Donázar, José A Revilla, Eloy Martín-López, Berta Gutiérrez-Cánovas, Cayetano Getz, Wayne M https://orcid.org/0000-0001-8784-9354 Morales-Reyes, Zebensui Campos-Arceiz, Ahimsa Crowder, Larry B Galetti, Mauro González-Suárez, Manuela He, Fengzhi Jordano, Pedro Lewison, Rebecca Naidoo, Robin Owen-Smith, Norman Selva, Nuria Svenning, Jens-Christian Tella, José L Zarfl, Christiane Jähnig, Sonja C Hayward, Matt W Faurby, Søren García, Nuria Barnosky, Anthony D Tockner, Klement https://escholarship.org/uc/item/41j4n2g3 The majority of variation in six traits critical to the growth, survival and reproduction of plant species is thought to be organised along just two dimensions, corresponding to strategies of plant size and resource acquisition. However, it is unknown whether global plant trait relationships extend to climatic extremes, and if these interspecific relationships are confounded by trait variation within species. We test whether trait relationships extend to the cold extremes of life on Earth using the largest database of tundra plant traits yet compiled. We show that tundra plants demonstrate remarkably similar resource economic traits, but not size traits, compared to global distributions, and exhibit the same two dimensions of trait variation. Three quarters of trait variation occurs among species, mirroring global estimates of interspecific trait variation. Plant trait relationships are thus generalizable to the edge of global trait-space, informing prediction of plant community... https://escholarship.org/uc/item/41j4n2g3 Sun, 18 Aug 2024 00:00:00 +0000 Thomas, HJD Bjorkman, AD Myers-Smith, IH Elmendorf, SC Kattge, J Diaz, S Vellend, M Blok, D Cornelissen, JHC Forbes, BC Henry, GHR Hollister, RD Normand, S Prevéy, JS Rixen, C Schaepman-Strub, G Wilmking, M Wipf, S Cornwell, WK Beck, PSA Georges, D Goetz, SJ Guay, KC Rüger, N Soudzilovskaia, NA Spasojevic, MJ https://orcid.org/0000-0003-1808-0048 Alatalo, JM Alexander, HD Anadon-Rosell, A Angers-Blondin, S te Beest, M Berner, LT Björk, RG Buchwal, A Buras, A Carbognani, M Christie, KS Collier, LS Cooper, EJ Elberling, B Eskelinen, A Frei, ER Grau, O Grogan, P Hallinger, M Heijmans, MMPD Hermanutz, L Hudson, JMG Johnstone, JF Hülber, K Iturrate-Garcia, M Iversen, CM Jaroszynska, F Kaarlejarvi, E Kulonen, A Lamarque, LJ Lantz, TC Lévesque, E Little, CJ Michelsen, A Milbau, A Nabe-Nielsen, J Nielsen, SS Ninot, JM Oberbauer, SF Olofsson, J Onipchenko, VG Petraglia, A Rumpf, SB Shetti, R Speed, JDM Suding, KN Tape, KD Tomaselli, M Trant, AJ Treier, UA Tremblay, M Venn, SE Vowles, T Weijers, S Wookey, PA Zamin, TJ Bahn, M Blonder, B https://orcid.org/0000-0002-5061-2385 van Bodegom, PM Bond-Lamberty, B Campetella, G Cerabolini, BEL Chapin, FS Craine, JM Dainese, M Green, WA Jansen, S Kleyer, M Manning, P Niinemets, Ü Onoda, Y Ozinga, WA Peñuelas, J Poschlod, P https://escholarship.org/uc/item/0q24d627 Abstract: Background and aims: Both drought and vegetation restoration can have dramatic effects on plant community composition, but how they influence soil microbial community diversity, structure, and co-occurrence networks remain less well known. Methods: To better understand the regulatory mechanisms of drought and vegetation restoration on soil microorganisms, we planted 12 native species in precipitation manipulation experimental plots in an invaded coastal grassland in California, USA. We measured soil bacterial and fungal community composition by amplicon sequencing, and quantified plant species richness and coverage in the third experimental year. Results: Our results showed that drought significantly altered soil bacterial diversity and composition; however, neither drought nor vegetation restoration had significant effects on fungal diversity and... https://escholarship.org/uc/item/0q24d627 Thu, 1 Aug 2024 00:00:00 +0000 Yang, Xuechen Loik, Michael E https://orcid.org/0000-0003-0847-6778 Wu, Xuefeng Luong, Justin C Wei, Xiaowei Li, Lu-Jun https://escholarship.org/uc/item/59m034ds Island faunas exhibit some of the most iconic examples where similar forms repeatedly evolve within different islands. Yet, whether these deterministic evolutionary trajectories within islands are driven by an initial, singular divergence and the subsequent exchange of individuals and adaptive genetic variation between islands remains unclear. Here, we study a gradual, repeated evolution of low-dispersive highland ecotypes from a dispersive lowland ecotype of <i>Calosoma</i> beetles along the island progression of the Galápagos. We show that repeated highland adaptation involved selection on multiple shared alleles within extensive chromosomal inversions that originated from an initial adaptation event on the oldest island. These highland inversions first spread through dispersal of highland individuals. Subsequent admixture with the lowland ecotype resulted in polymorphic dispersive populations from which the highland populations evolved on the youngest islands. Our findings... https://escholarship.org/uc/item/59m034ds Mon, 10 Jun 2024 00:00:00 +0000 Vangestel, Carl Swaegers, Janne De Corte, Zoë Dekoninck, Wouter Gharbi, Karim Gillespie, Rosemary https://orcid.org/0000-0003-0086-7424 Vandekerckhove, Matthias Van Belleghem, Steven M Hendrickx, Frederik https://escholarship.org/uc/item/0pd8s3ph Studies of adaptive radiations have played a central role in our understanding of reproductive isolation. Yet the focus has been on human-biased visual and auditory signals, leaving gaps in our knowledge of other modalities. To date, studies on chemical signals in adaptive radiations have focused on systems with multimodal signalling, making it difficult to isolate the role chemicals play in reproductive isolation. In this study we examine the use of chemical signals in the species recognition and adaptive radiation of Hawaiian <i>Tetragnatha</i> spiders by focusing on entire communities of co-occurring species, and conducting behavioural assays in conjunction with chemical analysis of their silks using gas chromatography-mass spectrometry. Male spiders significantly preferred the silk extracts of conspecific mates over those of sympatric heterospecifics. The compounds found in the silk extracts, long chain alkyl methyl ethers, were remarkably species-specific in the combination... https://escholarship.org/uc/item/0pd8s3ph Mon, 29 Apr 2024 00:00:00 +0000 Adams, Seira A https://orcid.org/0000-0003-1882-2806 Gurajapu, Anjali Qiang, Albert Gerbaulet, Moritz Schulz, Stefan Tsutsui, Neil D Ramirez, Santiago R https://orcid.org/0000-0003-1306-1315 Gillespie, Rosemary G https://orcid.org/0000-0003-0086-7424 https://escholarship.org/uc/item/9b95n9hm Abstract: Climate change will increase uncertainty in restoration outcomes due to greater water stress and other abiotic filters that limit plant survival. Drought‐related plant functional traits can help species withstand filters in a semi‐arid environment. Our objective was to provide guidance for selecting species to improve restoration success in a changing climate. We planted 12 native species in ambient rainfall and under 60% rain‐out shelters in an invaded coastal grassland in central California. We measured survival and size annually for 4&nbsp;years and quantified plant community and trait composition in the third and fourth years. We measured growth rate, specific leaf area (SLA), leaf C:N, leaf lobedness and leaf δ13C of all planted species and dominant extant species, and evaluated the effect of treatments, traits and phylogenetics on mortality risk using Cox proportional hazards. Native perennial species cover was greater, whereas thatch depth and per cent... https://escholarship.org/uc/item/9b95n9hm Sat, 13 Apr 2024 00:00:00 +0000 Luong, Justin C Holl, Karen D https://orcid.org/0000-0003-2893-6161 Loik, Michael E https://orcid.org/0000-0003-0847-6778 https://escholarship.org/uc/item/62q6q5zc Extensive evidence shows that regional (gamma) diversity is often lower across restored landscapes than in reference landscapes, in part due to common restoration practices that favor widespread species through selection of easily-grown species with high survival and propagation practices that reduce genetic diversity. We discuss approaches to counteract biotic homogenization, such as reintroducing species that are adapted to localized habitat conditions and are unlikely to colonize naturally; periodically reintroducing propagules from remnant populations to increase genetic diversity; and reintroducing higher trophic level fauna to restore interaction networks and processes that promote habitat heterogeneity. Several policy changes would also increase regional diversity; these include regional coordination amongst restoration groups, financial incentives to organizations producing conservation-valued species, and experimental designations for rare species introductions. https://escholarship.org/uc/item/62q6q5zc Sat, 13 Apr 2024 00:00:00 +0000 Holl, Karen D https://orcid.org/0000-0003-2893-6161 Luong, Justin C https://orcid.org/0000-0003-2118-4788 Brancalion, Pedro HS https://escholarship.org/uc/item/9xm181vd As climate change unfolds, changes in population dynamics and species distribution ranges are expected to fundamentally reshuffle communities worldwide. Yet, a comprehensive understanding of the mechanisms and extent of community reorganization remains elusive. This is particularly true in riverine systems, which are simultaneously exposed to changing temperature and streamflow, and where land-use change continues to be a major driver of biodiversity loss. Here, we use the most comprehensive compilation of fish abundance time series to date to provide a global synthesis of climate- and LU-induced effects on riverine biota with respect to changes in species thermal and streamflow affinities. We demonstrate that fish communities are increasingly dominated by thermophilic (warm-water) and limnophilic (slow-water) species. Despite being consistent with trends in water temperature and streamflow observed over recent decades, these community changes appear largely decoupled from each... https://escholarship.org/uc/item/9xm181vd Thu, 11 Apr 2024 00:00:00 +0000 Comte, Lise Olden, Julian D Tedesco, Pablo A Ruhi, Albert https://orcid.org/0000-0003-4011-6457 Giam, Xingli https://escholarship.org/uc/item/7426z73x Climate change is affecting the phenology of organisms and ecosystem processes across a wide range of environments. However, the links between organismal and ecosystem process change in complex communities remain uncertain. In snow-dominated watersheds, snowmelt in the spring and early summer, followed by a long low-flow period, characterizes the natural flow regime of streams and rivers. Here, we examined how earlier snowmelt will alter the phenology of mountain stream organisms and ecosystem processes via an outdoor mesocosm experiment in stream channels in the Eastern Sierra Nevada, California. The low-flow treatment, simulating a 3- to 6-wk earlier return to summer baseflow conditions projected under climate change scenarios in the region, increased water temperature and reduced biofilm production to respiration ratios by 32%. Additionally, most of the invertebrate species explaining community change (56% and 67% of the benthic and emergent taxa, respectively), changed in... https://escholarship.org/uc/item/7426z73x Thu, 11 Apr 2024 00:00:00 +0000 Leathers, Kyle Herbst, David de Mendoza, Guillermo Doerschlag, Gabriella Ruhi, Albert https://orcid.org/0000-0003-4011-6457 https://escholarship.org/uc/item/65r754sm River flows connect people, places, and other forms of life, inspiring and sustaining diverse cultural beliefs, values, and ways of life. The concept of environmental flows provides a framework for improving understanding of relationships between river flows and people, and for supporting those that are mutually beneficial. Nevertheless, most approaches to determining environmental flows remain grounded in the biophysical sciences. The newly revised Brisbane Declaration and Global Action Agenda on Environmental Flows (2018) represents a new phase in environmental flow science and an opportunity to better consider the co-constitution of river flows, ecosystems, and society, and to more explicitly incorporate these relationships into river management. We synthesize understanding of relationships between people and rivers as conceived under the renewed definition of environmental flows. We present case studies from Honduras, India, Canada, New Zealand, and Australia that illustrate... https://escholarship.org/uc/item/65r754sm Thu, 11 Apr 2024 00:00:00 +0000 Anderson, Elizabeth P Jackson, Sue Tharme, Rebecca E Douglas, Michael Flotemersch, Joseph E Zwarteveen, Margreet Lokgariwar, Chicu Montoya, Mariana Wali, Alaka Tipa, Gail T Jardine, Timothy D Olden, Julian D Cheng, Lin Conallin, John Cosens, Barbara Dickens, Chris Garrick, Dustin Groenfeldt, David Kabogo, Jane Roux, Dirk J Ruhi, Albert https://orcid.org/0000-0003-4011-6457 Arthington, Angela H https://escholarship.org/uc/item/5v51n6g8 Despite its far-reaching implications for conservation and natural resource management, little is known about the color of environmental noise, or the structure of temporal autocorrelation in random environmental variation, in streams and rivers. Here, we analyze the geography, drivers, and timescale-dependence of noise color in streamflow across the U.S. hydrography, using streamflow time&nbsp;series from 7504 gages. We find that daily and annual flows are dominated by red and white spectra respectively, and spatial variation in noise color is explained by a combination of geographic, hydroclimatic, and anthropogenic variables. Noise color at the daily scale is influenced by stream network position, and land use and water management explain around one third of the spatial variation in noise color irrespective of the timescale considered. Our results highlight the peculiarities of environmental variation regimes in riverine systems, and reveal a strong human fingerprint on the... https://escholarship.org/uc/item/5v51n6g8 Thu, 11 Apr 2024 00:00:00 +0000 Tu, Tongbi Comte, Lise Ruhi, Albert https://orcid.org/0000-0003-4011-6457 https://escholarship.org/uc/item/5g6565t0 Dendritic habitats, such as river ecosystems, promote the persistence of species by favouring spatial asynchronous dynamics among branches. Yet, our understanding of how network topology influences metapopulation synchrony in these ecosystems remains limited. Here, we introduce the concept of fluvial synchrogram to formulate and test expectations regarding the geography of metapopulation synchrony across watersheds. By combining theoretical simulations and an extensive fish population time-series dataset across Europe, we provide evidence that fish metapopulations can be buffered against synchronous dynamics as a direct consequence of network connectivity and branching complexity. Synchrony was higher between populations connected by direct water flow and decayed faster with distance over the Euclidean than the watercourse dimension. Likewise, synchrony decayed faster with distance in headwater than mainstem populations of the same basin. As network topology and flow directionality... https://escholarship.org/uc/item/5g6565t0 Thu, 11 Apr 2024 00:00:00 +0000 Larsen, Stefano Comte, Lise Filipe, Ana Filipa Fortin, Marie‐Josée Jacquet, Claire Ryser, Remo Tedesco, Pablo A Brose, Ulrich Erős, Tibor Giam, Xingli Irving, Katie Ruhi, Albert https://orcid.org/0000-0003-4011-6457 Sharma, Sapna Olden, Julian D https://escholarship.org/uc/item/1qp5k09b Biota in disturbance-prone landscapes have evolved a variety of strategies to persist long term, either locally (resistance) or by regional recolonization (resilience). Habitat fragmentation and isolation can limit the availability of recolonization pathways, and thus the dynamics of post-disturbance community reestablishment. However, empirical studies on how isolation may control the mechanisms that enable community recovery remain scarce. Here, we studied a pristine intermittent stream (Chalone Creek, Pinnacles National Park, California) to understand how isolation (distance from a perennial pool) alters invertebrate community recolonization after drying. We monitored benthic invertebrate reestablishment during the rewetting phase along a ~2-km gradient of isolation, using mesh traps that selected for specific recolonization pathways (i.e., drift, flying, swimming/crawling, and vertical migration from the hyporheic). We collected daily emigration samples, surveyed the reestablished... https://escholarship.org/uc/item/1qp5k09b Thu, 11 Apr 2024 00:00:00 +0000 Fournier, Robert de Mendoza, Guillermo Sarremejane, Romain Ruhi, Albert https://escholarship.org/uc/item/8v19v4bm The evolution of pre-zygotic reproductive isolation is a key step in the process of speciation. In many organisms, particularly insects, chemical labels are used as pheromones for species-specific mate recognition. Although an enormous body of knowledge exists regarding the patterns of pheromone chemical ecology, much less is known about the evolutionary processes that underlie the origin of new mating pheromones. Here, we examine case studies that have illuminated the origins of species-specific mating pheromones and suggest future directions for productive research. This article is part of the theme issue 'Signal detection theory in recognition systems: from evolving models to experimental tests'. https://escholarship.org/uc/item/8v19v4bm Mon, 8 Apr 2024 00:00:00 +0000 Adams, Seira Ashley https://orcid.org/0000-0003-1882-2806 Tsutsui, Neil Durie https://escholarship.org/uc/item/9vh0079w Large-scale studies on community ecology are highly desirable but often difficult to accomplish due to the considerable investment of time, labor and, money required to characterize richness, abundance, relatedness, and interactions. Nonetheless, such large-scale perspectives are necessary for understanding the composition, dynamics, and resilience of biological communities. Small invertebrates play a central role in ecosystems, occupying critical positions in the food web and performing a broad variety of ecological functions. However, it has been particularly difficult to adequately characterize communities of these animals because of their exceptionally high diversity and abundance. Spiders in particular fulfill key roles as both predator and prey in terrestrial food webs and are hence an important focus of ecological studies. In recent years, large-scale community analyses have benefitted tremendously from advances in DNA barcoding technology. High-throughput sequencing (HTS),... https://escholarship.org/uc/item/9vh0079w Sun, 7 Apr 2024 00:00:00 +0000 Kennedy, Susan R Prost, Stefan Overcast, Isaac Rominger, Andrew J Gillespie, Rosemary G https://orcid.org/0000-0003-0086-7424 Krehenwinkel, Henrik https://escholarship.org/uc/item/99s1c1cw We describe a new pathway for multivariate analysis of data consisting of counts of species abundances that includes two key components: copulas, to provide a flexible joint model of individual species, and dissimilarity-based methods, to integrate information across species and provide a holistic view of the community. Individual species are characterized using suitable (marginal) statistical distributions, with the mean, the degree of over-dispersion, and/or zero-inflation being allowed to vary among a priori groups of sampling units. Associations among species are then modeled using copulas, which allow any pair of disparate types of variables to be coupled through their cumulative distribution function, while maintaining entirely the separate individual marginal distributions appropriate for each species. A Gaussian copula smoothly captures changes in an index of association that excludes joint absences in the space of the original species variables. A permutation-based filter... https://escholarship.org/uc/item/99s1c1cw Thu, 28 Mar 2024 00:00:00 +0000 Anderson, Marti J de Valpine, Perry https://orcid.org/0000-0002-8329-6796 Punnett, Andrew Miller, Arden E https://escholarship.org/uc/item/976752d6 Population dynamics are functions of several demographic processes including survival, reproduction, somatic growth, and maturation. The rates or probabilities for these processes can vary by time, by location, and by individual. These processes can co-vary and interact to varying degrees, e.g., an animal can only reproduce when it is in a particular maturation state. Population dynamics models that treat the processes as independent may yield somewhat biased or imprecise parameter estimates, as well as predictions of population abundances or densities. However, commonly used integral projection models (IPMs) typically assume independence across these demographic processes. We examine several approaches for modelling between process dependence in IPMs and include cases where the processes co-vary as a function of time (temporal variation), co-vary within each individual (individual heterogeneity), and combinations of these (temporal variation and individual heterogeneity). We... https://escholarship.org/uc/item/976752d6 Thu, 28 Mar 2024 00:00:00 +0000 Fung, Yik Leung Newman, Ken King, Ruth de Valpine, Perry https://orcid.org/0000-0002-8329-6796 https://escholarship.org/uc/item/2cc268w9 The ongoing recovery of terrestrial large carnivores in North America and Europe is accompanied by intense controversy. On the one hand, reestablishment of large carnivores entails a recovery of their most important ecological role, predation. On the other hand, societies are struggling to relearn how to live with apex predators that kill livestock, compete for game species, and occasionally injure or kill people. Those responsible for managing these species and mitigating conflict often lack fundamental information due to a long-standing challenge in ecology: How do we draw robust population-level inferences for elusive animals spread over immense areas? Here we showcase the application of an effective tool for spatially explicit tracking and forecasting of wildlife population dynamics at scales that are relevant to management and conservation. We analyzed the world's largest dataset on carnivores comprising more than 35,000 noninvasively obtained DNA samples from over 6,000... https://escholarship.org/uc/item/2cc268w9 Thu, 28 Mar 2024 00:00:00 +0000 Bischof, Richard Milleret, Cyril Dupont, Pierre Chipperfield, Joseph Tourani, Mahdieh Ordiz, Andrés de Valpine, Perry https://orcid.org/0000-0002-8329-6796 Turek, Daniel Royle, J Andrew Gimenez, Olivier Flagstad, Øystein Åkesson, Mikael Svensson, Linn Brøseth, Henrik Kindberg, Jonas https://escholarship.org/uc/item/27n6f705 Identifying rates at which birders engage with different species can inform the impact and efficacy of conservation outreach and the scientific use of community-collected biodiversity data. Species that are thought to be “charismatic” are often prioritized in conservation, and previous researchers have used sociological experiments and digital records to estimate charisma indirectly. In this study, we take advantage of community science efforts as another record of human engagement with animals that can reveal observer biases directly, which are in part driven by observer preference. We apply a multistage analysis to ask whether opportunistic birders contributing to iNaturalist engage more with larger, more colorful, and rarer birds relative to a baseline approximated from eBird contributors. We find that body mass, color contrast, and range size all predict overrepresentation in the opportunistic dataset. We also find evidence that, across 472 modeled species, 52 species are... https://escholarship.org/uc/item/27n6f705 Thu, 28 Mar 2024 00:00:00 +0000 Stoudt, Sara Goldstein, Benjamin R de Valpine, Perry https://orcid.org/0000-0002-8329-6796 https://escholarship.org/uc/item/20x8387c Spatial capture-recapture (SCR) is now routinely used for estimating abundance and density of wildlife populations. A standard SCR model includes sub-models for the distribution of individual activity centers (ACs) and for individual detections conditional on the locations of these ACs. Both sub-models can be expressed as point processes taking place in continuous space, but there is a lack of accessible and efficient tools to fit such models in a Bayesian paradigm. Here, we describe a set of custom functions and distributions to achieve this. Our work allows for more efficient model fitting with spatial covariates on population density, offers the option to fit SCR models using the semi-complete data likelihood (SCDL) approach instead of data augmentation, and better reflects the spatially continuous detection process in SCR studies that use area searches. In addition, the SCDL approach is more efficient than data augmentation for simple SCR models while losing its advantages... https://escholarship.org/uc/item/20x8387c Thu, 28 Mar 2024 00:00:00 +0000 Zhang, Wei Chipperfield, Joseph D Illian, Janine B Dupont, Pierre Milleret, Cyril de Valpine, Perry https://orcid.org/0000-0002-8329-6796 Bischof, Richard https://escholarship.org/uc/item/17t1x6w5 Open-population spatial capture-recapture (OPSCR) models use the spatial information contained in individual detections collected over multiple consecutive occasions to estimate not only occasion-specific density, but also demographic parameters. OPSCR models can also estimate spatial variation in vital rates, but such models are neither widely used nor thoroughly tested. We developed a Bayesian OPSCR model that not only accounts for spatial variation in survival using spatial covariates but also estimates local density-dependent effects on survival within a unified framework. Using simulations, we show that OPSCR models provide sound inferences on the effect of spatial covariates on survival, including multiple competing sources of mortality, each with potentially different spatial determinants. Estimation of local density-dependent survival was possible but required more data due to the greater complexity of the model. Not accounting for spatial heterogeneity in survival led... https://escholarship.org/uc/item/17t1x6w5 Thu, 28 Mar 2024 00:00:00 +0000 Milleret, Cyril Dey, Soumen Dupont, Pierre Brøseth, Henrik Turek, Daniel de Valpine, Perry https://orcid.org/0000-0002-8329-6796 Bischof, Richard https://escholarship.org/uc/item/01k9403b To analyze species count data when detection is imperfect, ecologists need models to estimate relative abundance in the presence of unknown sources of heterogeneity. Two candidate models are generalized linear mixed models (GLMMs) and hierarchical N-mixture models. GLMMs are computationally robust but do not explicitly separate detection from abundance patterns. N-mixture models separately estimate detection and abundance via a latent state but are sensitive to violations in assumptions and subject to practical estimation issues. When one can assume that detection is not systematically confounded with ecological patterns of interest, these two models can be viewed as sharing a heuristic framework for relative abundance estimation. Model selection can then&nbsp;determine which predicts observed counts best, for example by AIC. We compared four N-mixture model variants and two GLMM variants for predicting bird counts in local subsets of a citizen science dataset, eBird, based on... https://escholarship.org/uc/item/01k9403b Thu, 28 Mar 2024 00:00:00 +0000 Goldstein, Benjamin R de Valpine, Perry https://orcid.org/0000-0002-8329-6796 https://escholarship.org/uc/item/6109w3mt Data that influence policy and major investment decisions risk entrenching social and political inequities. https://escholarship.org/uc/item/6109w3mt Wed, 27 Mar 2024 00:00:00 +0000 Chapman, Melissa Goldstein, Benjamin R Schell, Christopher J https://orcid.org/0000-0002-2073-9852 Brashares, Justin S Carter, Neil H Ellis-Soto, Diego Faxon, Hilary Oliva Goldstein, Jenny E Halpern, Benjamin S Longdon, Joycelyn Norman, Kari EA O'Rourke, Dara Scoville, Caleb Xu, Lily Boettiger, Carl https://escholarship.org/uc/item/1cc0c4tw The Morrill Act of 1862 established agricultural and mechanical arts colleges by granting public lands to states to promote the liberal and practical education of (white, male, Christian) U.S. citizens of average means. In this paper, I use Charles Mills’ (1997) Racial Contract framework and Patrick Wolfe’s (2007) concept of <em>corpus nullius </em>to situate the Morrill Act in a white supremacist political system that intimately entwined settler-colonial expansion, agricultural knowledge production, and the founding of U.S. public higher education through creation of the land-grant universities. https://escholarship.org/uc/item/1cc0c4tw Thu, 29 Feb 2024 00:00:00 +0000 Fanshel, Rosalie Z https://escholarship.org/uc/item/6jn9h3f5 Adaptive radiation plays a fundamental role in our understanding of the evolutionary process. However, the concept has provoked strong and differing opinions concerning its definition and nature among researchers studying a wide diversity of systems. Here, we take a broad view of what constitutes an adaptive radiation, and seek to find commonalities among disparate examples, ranging from plants to invertebrate and vertebrate animals, and remote islands to lakes and continents, to better understand processes shared across adaptive radiations. We surveyed many groups to evaluate factors considered important in a large variety of species radiations. In each of these studies, ecological opportunity of some form is identified as a prerequisite for adaptive radiation. However, evolvability, which can be enhanced by hybridization between distantly related species, may play a role in seeding entire radiations. Within radiations, the processes that lead to speciation depend largely on... https://escholarship.org/uc/item/6jn9h3f5 Sun, 25 Feb 2024 00:00:00 +0000 Gillespie, Rosemary G https://orcid.org/0000-0003-0086-7424 Bennett, Gordon M De Meester, Luc Feder, Jeffrey L Fleischer, Robert C Harmon, Luke J Hendry, Andrew P Knope, Matthew L Mallet, James Martin, Christopher https://orcid.org/0000-0001-7989-9124 Parent, Christine E Patton, Austin H Pfennig, Karin S Rubinoff, Daniel Schluter, Dolph Seehausen, Ole Shaw, Kerry L Stacy, Elizabeth Stervander, Martin Stroud, James T Wagner, Catherine Wogan, Guinevere OU https://escholarship.org/uc/item/4fj9n31r Carpenter ants in the genus Camponotus are large, conspicuous ants that are abundant and ecologically influential in many terrestrial ecosystems. The bicolored carpenter ant, Camponotus vicinus Mayr, is distributed across a wide range of elevations and latitudes in western North America, where it is a prominent scavenger and predator. Here, we present a high-quality genome assembly of C. vicinus from a sample collected in Sonoma County, California, near the type locality of the species. This genome assembly consists of 38 scaffolds spanning 302.74 Mb, with contig N50 of 15.9 Mb, scaffold N50 of 19.9 Mb, and BUSCO completeness of 99.2%. This genome sequence will be a valuable resource for exploring the evolutionary ecology of C. vicinus and carpenter ants generally. It also provides an important tool for clarifying cryptic diversity within the C. vicinus species complex, a genetically diverse set of populations, some of which are quite localized and of conservation interest. https://escholarship.org/uc/item/4fj9n31r Thu, 15 Feb 2024 00:00:00 +0000 Ward, Philip S https://orcid.org/0000-0002-9019-0383 Cash, Elizabeth I https://orcid.org/0000-0002-1192-3770 Ferger, Kailey Escalona, Merly https://orcid.org/0000-0003-0213-4777 Sahasrabudhe, Ruta Miller, Courtney Toffelmier, Erin https://orcid.org/0000-0001-6028-8497 Fairbairn, Colin Seligmann, William https://orcid.org/0000-0002-5762-3095 Shaffer, H Bradley Tsutsui, Neil D https://escholarship.org/uc/item/12w4g830 Lessons learned from an interdisciplinary evaluation of long-term restoration outcomes on 37 restored coastal grasslands in California https://escholarship.org/uc/item/12w4g830 Thu, 1 Feb 2024 00:00:00 +0000 Luong, Justin C Press, Daniel M Holl, Karen D https://orcid.org/0000-0003-2893-6161 https://escholarship.org/uc/item/5hk1j679 The fossil record suggests some insect species have a marked longevity. The oldest fossils purported to represent extant insect species are from the Oligocene and Eocene. One of the most cited fossils is the extant tiger beetle Tetracha carolina (Coleoptera: Cicindelidae) that was identified over a century ago by Walther Horn in Eocene Baltic amber. We examined this and compared it to the previously described cincindelid Baltic amber fossil Palaeoiresina cassolai using X-ray microscopy and 3D imaging techniques. We conclude that Horn’s fossil tiger beetle specimen is conspecific with the Eocene P. cassolai and is a member of an extinct stem group lineage of Cicindelidae. Based on a review of all the tiger beetle fossils described from Cretaceous and Paleogene deposits, we found that the assignment of these fossil species to extant lineages is not supported. There are currently no synapomorphies known from fossils that can provide evidence for Cretaceous Manticorni or Megacephalini... https://escholarship.org/uc/item/5hk1j679 Mon, 15 Jan 2024 00:00:00 +0000 Schmidt, Joachim Scholz, Stephan Wiesner, Jürgen Will, Kipling https://orcid.org/0000-0002-7056-9011 https://escholarship.org/uc/item/7rn021p8 A new species of the carabid beetle genus <i>Bembidion</i> Latreille is described from the Central Valley, Los Angeles Basin, and surrounding areas of California. <i>Bembidionbrownorum</i><b>sp. nov.</b> is a distinctive species, a relatively large member of the subgenus Notaphus Dejean, and within <i>Notaphus</i> a member of the <i>B.obtusangulum</i> LeConte species group. It has faint spots on the elytra and a large, convex, rounded prothorax. Of the 22 specimens from 11 localities, all but one were collected more than 55 years ago. Although the collection of the holotype in 2021 at UV light suggest the species is still extant, the lack of other recent specimens suggests the species may have a more restricted distribution than in the past, and its populations may be in decline. https://escholarship.org/uc/item/7rn021p8 Tue, 9 Jan 2024 00:00:00 +0000 Maddison, David R Sproul, John S Will, Kipling https://orcid.org/0000-0002-7056-9011 https://escholarship.org/uc/item/6968h58g The Oodini precinctive to New Caledonia are reviewed with nine species recognized, of which seven are newly described in two genera. Five species are described in the genus <i>Coptocarpus</i> Chaudoir: <i>C. microps</i> <b>sp. nov.</b>, <i>C. erwini</i> <b>sp. nov.</b>, <i>C. amieuensis</i> <b>sp. nov.</b>, <i>C. magnus</i> <b>sp. nov.</b>, and <i>C. lescheni</i> <b>sp. nov.</b> In the genus <i>Adelopomorpha</i> Heller two species, <i>A. tethys</i> <b>sp. nov.</b> and <i>A. tuberculata</i> <b>sp. nov.</b>, are described. In order to place cladistically the newly described species in a genus, a phylogenetic analysis of a matrix of 36 characters of adult morphology was conducted including exemplar species of three putative outgroup genera, six putative ingroup thryptocerine oodine genera, and all oodine species from New Caledonia. Results show support for Thryptocerina and monophyly of <i>Adelopomorpha</i>. <i>Hoplolenus</i> LaFerté-Sénectère is not monophyletic and <i>Hoplolenus... https://escholarship.org/uc/item/6968h58g Tue, 9 Jan 2024 00:00:00 +0000 Will, Kipling https://orcid.org/0000-0002-7056-9011 Guéorguiev, Borislav https://escholarship.org/uc/item/6167s7v4 Host-associated microbiomes can play important roles in the ecology and evolution of their insect hosts, but bacterial diversity in many insect groups remains poorly understood. Here we examine the relationship between host environment, host traits, and microbial diversity in three species in the ground beetle family (Coleoptera: Carabidae), a group of roughly 40,000 species that synthesize a wide diversity of defensive compounds. This study used 16S amplicon sequencing to profile three species that are phylogenetically distantly related, trophically distinct, and whose defensive chemical secretions differ: Anisodactylus similis LeConte, 1851, Pterostichus serripes (LeConte, 1875), and Brachinus elongatulus Chaudoir, 1876. Wild-caught beetles were compared to individuals maintained in the lab for two weeks on carnivorous, herbivorous, or starvation diets (n = 3 beetles for each species-diet combination). Metagenomic samples from two highly active tissue types-guts, and pygidial... https://escholarship.org/uc/item/6167s7v4 Tue, 9 Jan 2024 00:00:00 +0000 Silver, Anita Perez, Sean Gee, Melanie Xu, Bethany Garg, Shreeya Will, Kipling https://orcid.org/0000-0002-7056-9011 Gill, Aman https://escholarship.org/uc/item/0h84d9s2 We found distinct and consistently placed, species- and sex-specific abrasions of the cuticle on museum specimens of 14 species of the <i>Pterostichus</i> Bonelli, 1810 (Carabidae, Pterostichini) subgenusHypherpes Chaudoir, 1838. We deduced that these marks are generated during mating and, therefore, can be used to distinguish between preserved specimens of beetles that had previously mated at the time of capture and those that had not mated. In addition to describing and detailing the occurrence of the marks and providing evidence that they are the result of mating, we demonstrate their utility for inferring life history using a museum voucher collection. By scoring these indications of mating from pinned specimens, we describe life cycle patterns in two similar, relatively closely related and sympatric species of the subgenus <i>Hypherpes, P.vicinus</i> Mannerheim, 1843 and <i>P.californicus</i> (Dejean, 1828). Both were sampled during a pitfall trap study in Contra Costa, California,... https://escholarship.org/uc/item/0h84d9s2 Tue, 9 Jan 2024 00:00:00 +0000 Will, Kipling https://orcid.org/0000-0002-7056-9011 Mendez, Patina K https://escholarship.org/uc/item/8cw1965z This paper reviews Drosophila voltage-gated Na(+) channel mutations encoded by the para (paralytic) gene and their contributions to seizure disorders in the fly. Numerous mutations cause seizure-sensitivity, for example, para(bss1), with phenotypes that resemble human intractable epilepsy in some aspects. Seizure phenotypes are also seen with human GEFS+ spectrum mutations that have been knocked into the Drosophila para gene, para(GEFS+) and para(DS) alleles. Other para mutations, para(ST76) and para(JS) act as seizure-suppressor mutations reverting seizure phenotypes in other mutants. Seizure-like phenotypes are observed from mutations and other conditions that cause a persistent Na(+) current through either changes in mRNA splicing or protein structure. https://escholarship.org/uc/item/8cw1965z Sun, 24 Dec 2023 00:00:00 +0000 Kroll, Jason R Saras, Arunesh Tanouye, Mark A https://escholarship.org/uc/item/5q16f79v Pathogen evasion of the host immune system is a key force driving extreme polymorphism in genes of the major histocompatibility complex (MHC). Although this gene family is well characterized in structure and function, there is still much debate surrounding the mechanisms by which MHC diversity is selectively maintained. Many studies have investigated relationships between MHC variation and specific pathogens, and have found mixed support for and against the hypotheses of heterozygote advantage, frequency-dependent or fluctuating selection. Few, however, have focused on the selective effects of multiple parasite types on host immunogenetic patterns. Here, we examined relationships between variation in the equine MHC gene, ELA-DRA, and both gastrointestinal (GI) and ectoparasitism in plains zebras (Equus quagga). Specific alleles present at opposing population frequencies had antagonistic effects, with rare alleles associated with increased GI parasitism and common alleles with... https://escholarship.org/uc/item/5q16f79v Sun, 24 Dec 2023 00:00:00 +0000 Kamath, Pauline L Turner, Wendy C Küsters, Martina Getz, Wayne M https://orcid.org/0000-0001-8784-9354 https://escholarship.org/uc/item/2qb962kv Pollinator-plant relationships are found to be particularly vulnerable to land use change. Yet despite extensive research in agricultural and natural systems, less attention has focused on these interactions in neighboring urban areas and its impact on pollination services. We investigated pollinator-plant interactions in a peri-urban landscape on the outskirts of the San Francisco Bay Area, California, where urban, agricultural, and natural land use types interface. We made standardized observations of floral visitation and measured seed set of yellow starthistle (Centaurea solstitialis), a common grassland invasive, to test the hypotheses that increasing urbanization decreases 1) rates of bee visitation, 2) viable seed set, and 3) the efficiency of pollination (relationship between bee visitation and seed set). We unexpectedly found that bee visitation was highest in urban and agricultural land use contexts, but in contrast, seed set rates in these human-altered landscapes were... https://escholarship.org/uc/item/2qb962kv Sun, 24 Dec 2023 00:00:00 +0000 Leong, Misha Kremen, Claire Roderick, George K https://orcid.org/0000-0001-7557-2415 https://escholarship.org/uc/item/2d76453t Homologous recombination plays a key function in the evolution of bacterial genomes. Within Xylella fastidiosa, an emerging plant pathogen with increasing host and geographic ranges, it has been suggested that homologous recombination facilitates host switching, speciation, and the development of virulence. We used 340 whole-genome sequences to study the relationship between inter- and intrasubspecific homologous recombination, random mutation, and natural selection across individual X. fastidiosa genes. Individual gene orthologs were identified and aligned, and a maximum likelihood (ML) gene tree was generated. Each gene alignment and tree pair were then used to calculate gene-wide and branch-specific <i>r/m</i> values (relative effect of recombination to mutation), gene-wide and branch-site nonsynonymous over synonymous substitution rates (d<i>N</i>/d<i>S</i> values; episodic selection), and branch length (as a proxy for mutation rate). The relationships between these variables... https://escholarship.org/uc/item/2d76453t Wed, 15 Nov 2023 00:00:00 +0000 Castillo, Andreina I Almeida, Rodrigo PP https://orcid.org/0000-0003-2888-9617 https://escholarship.org/uc/item/679294sf While it is recognized that farming alternatively is inherently knowledge intensive, in the United States, farmer knowledge has been widely overlooked and under-documented within the scientific literature. Farmer knowledge of soil in particular is understudied in the US, especially given that healthy soils have been identified as the basis for resilient agriculture. Applying an exploratory, case study approach, we interviewed 13 organic farmers based in Yolo County, California to understand how organic farmers in this region acquire knowledge about their soils, to document what organic farmers in this region know about their soils, and to share key management practices organic farmers use to build soil health in the region. We found the organic farmers in this study acquire knowledge about their farming systems primarily through direct observation, personal experience, experimentation, and inherited wisdom. To evaluate soil health, farmers in this study cited using a range of... https://escholarship.org/uc/item/679294sf Wed, 8 Nov 2023 00:00:00 +0000 Klein, Ansel Olive Carlisle, Liz Lloyd, Margaret G Sayre, Nathan F https://orcid.org/0000-0002-9243-2219 Bowles, Timothy M https://escholarship.org/uc/item/4ms2w7ww The pathogen <i>Xylella fastidiosa</i> subsp. <i>fastidiosa</i> has circulated through California's vineyards since its introduction from Central America in the 1800s. This pathogen is responsible for a bacterial disease called Pierce's disease (PD) of grapevine. With no known cure, PD has had devastating effects on some vineyards. Important factors that impact disease severity and persistence include: the presence of insect vectors, grapevine cultivar, management, ecology, and winter temperatures. Removal of infected vines is critical for reducing pathogen spread but relies on accurate and rapid pathogen detection. In this study, we foster a greater understanding of disease symptom emergence by way of a 3-year field inoculation project in Napa Valley. Although PD emergence and symptom progression have been studied in greenhouse and experimental plots, there is a large knowledge gap in quantifying disease progression under commercial conditions. After inoculating 80 mature <i>Vitis... https://escholarship.org/uc/item/4ms2w7ww Wed, 8 Nov 2023 00:00:00 +0000 Kahn, Alexandra K Sicard, Anne Cooper, Monica L https://orcid.org/0000-0003-1465-6142 Daugherty, Matthew P Donegan, Monica A Almeida, Rodrigo PP https://orcid.org/0000-0003-2888-9617 https://escholarship.org/uc/item/2wz4q4tf Onthophagus taurus Increases Soil Microbes Associated with Nutrient Cycling in California Pastureland Soils https://escholarship.org/uc/item/2wz4q4tf Mon, 30 Oct 2023 00:00:00 +0000 Lipton, Suzanne Meyer, Rachel S Richardson, Greg Philpott, Stacy M https://escholarship.org/uc/item/9d53c4bb BackgroundUnderstanding rhino movement behavior, especially their recursive movements, holds significant promise for enhancing rhino conservation efforts, and protecting their habitats and the biodiversity they support. Here we investigate the daily, biweekly, and seasonal recursion behavior of rhinos, to aid conservation applications and increase our foundational knowledge about these important ecosystem engineers.MethodsUsing relocation data from 59 rhinos across northern Namibia and 8 years of sampling efforts, we investigated patterns in 24-h displacement at dawn, dusk, midday, and midnight to examine movement behaviors at an intermediate scale and across daily behavioral modes of foraging and resting. To understand recursion patterns across animals’ short and long-term ranges, we built T-LoCoH time use grids to estimate recursive movement by each individual. Comparing these grids to contemporaneous MODIS imagery, we investigated productivity’s influence on short-term space... https://escholarship.org/uc/item/9d53c4bb Sun, 22 Oct 2023 00:00:00 +0000 Seidel, Dana Paige Linklater, Wayne L Kilian, Werner Preez, Pierre du Getz, Wayne M https://orcid.org/0000-0001-8784-9354 https://escholarship.org/uc/item/9b4969pw Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to the spread of modern humans into the rest of Eurasia and their replacement of the Neanderthals. That the inter-species boundary remained geographically localized for so long is a puzzle, particularly in light of the rapidity of its subsequent movement. Here, we propose that infectious-disease dynamics can explain the localization and persistence of the inter-species boundary. We further propose, and support with dynamical-systems models, that introgression-based&nbsp;transmission of alleles related to the immune system would have gradually diminished this barrier to pervasive inter-species interaction, leading to the eventual release of the inter-species boundary from its geographic localization. Asymmetries between the species in the characteristics of their associated ‘pathogen packages’ could have generated feedback that allowed modern humans to overcome disease burden earlier than... https://escholarship.org/uc/item/9b4969pw Sun, 22 Oct 2023 00:00:00 +0000 Greenbaum, Gili Getz, Wayne M https://orcid.org/0000-0001-8784-9354 Rosenberg, Noah A Feldman, Marcus W Hovers, Erella Kolodny, Oren https://escholarship.org/uc/item/7qf444r7 Bovine tuberculosis (BTB) is endemic to the African buffalo (Syncerus caffer) of Hluhluwe-iMfolozi Park (HiP) and Kruger National Park, South Africa. In HiP, the disease has been actively managed since 1999 through a test-and-cull procedure targeting BTB-positive buffalo. Prior studies in Kruger showed associations between microsatellite alleles, BTB and body condition. A sex chromosomal meiotic drive, a form of natural gene drive, was hypothesized to be ultimately responsible. These associations indicate high-frequency occurrence of two types of male-deleterious alleles (or multiple-allele haplotypes). One type negatively affects body condition and BTB resistance in both sexes. The other type has sexually antagonistic effects: negative in males but positive in females. Here, we investigate whether a similar gene drive system is present in HiP buffalo, using 17 autosomal microsatellites and microsatellite-derived Y-chromosomal haplotypes from 401 individuals, culled in 2002-2004.... https://escholarship.org/uc/item/7qf444r7 Sun, 15 Oct 2023 00:00:00 +0000 van Hooft, Pim Getz, Wayne M https://orcid.org/0000-0001-8784-9354 Greyling, Barend J Bastos, Armanda DS https://escholarship.org/uc/item/7wf5k89s Climate and land-use change could exhibit concordant effects that favor or disfavor the same species, which would amplify their impacts, or species may respond to each threat in a divergent manner, causing opposing effects that moderate their impacts in isolation. We used early 20th century surveys of birds conducted by Joseph Grinnell paired with modern resurveys and land-use change reconstructed from historic maps to examine avian change in Los Angeles and California's Central Valley (and their surrounding foothills). Occupancy and species richness declined greatly in Los Angeles from urbanization, strong warming (+1.8°C), and drying (-77.2&nbsp;millimeters) but remained stable in the Central Valley, despite large-scale agricultural development, average warming (+0.9°C), and increased precipitation (+11.2&nbsp;millimeters). While climate was the main driver of species distributions a century ago, the combined impacts of land-use and climate change drove temporal changes in occupancy,... https://escholarship.org/uc/item/7wf5k89s Fri, 29 Sep 2023 00:00:00 +0000 Beissinger, Steven R https://orcid.org/0000-0003-1323-2727 MacLean, Sarah A Iknayan, Kelly J de Valpine, Perry https://orcid.org/0000-0002-8329-6796 https://escholarship.org/uc/item/97s838d3 The implementation of intelligent software to identify and classify objects and individuals in visual fields is a technology of growing importance to operatives in many fields, including wildlife conservation and management. To non-experts, the methods can be abstruse and the results mystifying. Here, in the context of applying cutting edge methods to classify wildlife species from camera-trap data, we shed light on the methods themselves and types of features these methods extract to make efficient identifications and reliable classifications. The current state of the art is to employ convolutional neural networks (CNN) encoded within deep-learning algorithms. We outline these methods and present results obtained in training a CNN to classify 20 African wildlife species with an overall accuracy of 87.5% from a dataset containing 111,467 images. We demonstrate the application of a gradient-weighted class-activation-mapping (Grad-CAM) procedure to extract the most salient pixels... https://escholarship.org/uc/item/97s838d3 Wed, 20 Sep 2023 00:00:00 +0000 Miao, Zhongqi Gaynor, Kaitlyn M Wang, Jiayun Liu, Ziwei Muellerklein, Oliver Norouzzadeh, Mohammad Sadegh McInturff, Alex Bowie, Rauri CK https://orcid.org/0000-0001-8328-6021 Nathan, Ran Yu, Stella X Getz, Wayne M https://orcid.org/0000-0001-8784-9354 https://escholarship.org/uc/item/4k75r21z Dynamic SEIR (Susceptible, Exposed, Infectious, Removed) compartmental models provide a tool for predicting the size and duration of both unfettered and managed outbreaks-the latter in the context of interventions such as case detection, patient isolation, vaccination and treatment. The reliability of this tool depends on the validity of key assumptions that include homogeneity of individuals and spatio-temporal homogeneity. Although the SEIR compartmental framework can easily be extended to include demographic (e.g. age) and additional disease (e.g. healthcare workers) classes, dependence of transmission rates on time, and metapopulation structure, fitting such extended models is hampered by both a proliferation of free parameters and insufficient or inappropriate data. This raises the question of how effective a tool the basic SEIR framework may actually be. We go some way here to answering this question in the context of the 2014-2015 outbreak of Ebola in West Africa by comparing... https://escholarship.org/uc/item/4k75r21z Wed, 20 Sep 2023 00:00:00 +0000 Getz, Wayne M https://orcid.org/0000-0001-8784-9354 Salter, Richard Mgbara, Whitney https://escholarship.org/uc/item/2pt6n2vt How a disease is transmitted affects our ability to determine R₀, the average number of new cases caused by an infectious host at the onset of an epidemic. R₀ becomes progressively more difficult to compute as transmission varies from directly transmitted diseases to diseases that are vector-borne to environmentally transmitted diseases. Pathogens responsible for diseases with environmental transmission are typically maintained in environmental reservoirs that exhibit a complex spatial distribution of local infectious zones (LIZs). Understanding host encounters with LIZs and pathogen persistence within LIZs is required for an accurate R₀ and modeling these contacts requires an integrated geospatial and dynamical systems approach. Here we review how interactions between host and pathogen populations and environmental reservoirs are driven by landscape-level variables, and synthesize the quantitative framework needed to formulate outbreak response and disease control. https://escholarship.org/uc/item/2pt6n2vt Wed, 20 Sep 2023 00:00:00 +0000 Blackburn, Jason K Ganz, Holly H Ponciano, José Miguel Turner, Wendy C Ryan, Sadie J Kamath, Pauline Cizauskas, Carrie Kausrud, Kyrre Holt, Robert D Stenseth, Nils Chr Getz, Wayne M https://orcid.org/0000-0001-8784-9354 https://escholarship.org/uc/item/9dv6s3jp In light of the current biodiversity crisis, molecular barcoding has developed into an irreplaceable tool. Barcoding has been considerably simplified by developments in high throughput sequencing technology, but still can be prohibitively expensive and laborious when community samples of thousands of specimens need to be processed. Here, we outline an Illumina amplicon sequencing approach to generate multilocus data from large collections of arthropods. We reduce cost and effort up to 50-fold, by combining multiplex PCRs and DNA extractions from pools of presorted and morphotyped specimens and using two levels of sample indexing. We test our protocol by generating a comprehensive, community wide dataset of barcode sequences for several thousand Hawaiian arthropods from 14 orders, which were collected across the archipelago using various trapping methods. We explore patterns of diversity across the Archipelago and compare the utility of different arthropod trapping methods for... https://escholarship.org/uc/item/9dv6s3jp Thu, 17 Aug 2023 00:00:00 +0000 de Kerdrel, Guillemette A Andersen, Jeremy C Kennedy, Susan R Gillespie, Rosemary https://orcid.org/0000-0003-0086-7424 Krehenwinkel, Henrik https://escholarship.org/uc/item/8mm2r79m The relative influence of geography, currents, and environment on gene flow within sessile marine species remains an open question. Detecting subtle genetic differentiation at small scales is challenging in benthic populations due to large effective population sizes, general lack of resolution in genetic markers, and because barriers to dispersal often remain elusive. Marine lakes can circumvent confounding factors by providing discrete and replicated ecosystems. Using high-resolution double digest restriction-site-associated DNA sequencing (4826 Single Nucleotide Polymorphisms, SNPs), we genotyped populations of the sponge <i>Suberites diversicolor</i> (<i>n</i> = 125) to test the relative importance of spatial scales (1-1400 km), local environmental conditions, and permeability of seascape barriers in shaping population genomic structure. With the SNP dataset, we show strong intralineage population structure, even at scales &lt;10 km (average <i>F</i> _ST = 0.63),... https://escholarship.org/uc/item/8mm2r79m Thu, 17 Aug 2023 00:00:00 +0000 Maas, Diede L Prost, Stefan de Leeuw, Christiaan A Bi, Ke Smith, Lydia L https://orcid.org/0009-0005-8556-0246 Purwanto, Purwanto Aji, Ludi P Tapilatu, Ricardo F Gillespie, Rosemary G https://orcid.org/0000-0003-0086-7424 Becking, Leontine E https://escholarship.org/uc/item/8gc639nx Venom has been associated with the ecological success of many groups of organisms, most notably reptiles, gastropods, and arachnids. In some cases, diversification has been directly linked to tailoring of venoms for dietary specialization. Spiders in particular are known for their diverse venoms and wide range of predatory behaviors, although there is much to learn about scales of variation in venom composition and function. The current study focuses on venom characteristics in different sexes within a species of spider. We chose the genus <i>Tetragnatha</i> (Tetragnathidae) because of its unusual courtship behavior involving interlocking of the venom delivering chelicerae (i.e., the jaws), and several species in the genus are already known to have sexually dimorphic venoms. Here, we use transcriptome and proteome analyses to identify venom components that are dimorphic in <i>Tetragnatha versicolor</i>. We present cDNA sequences including unique, male-specific high molecular weight... https://escholarship.org/uc/item/8gc639nx Thu, 17 Aug 2023 00:00:00 +0000 Zobel-Thropp, Pamela A Bulger, Emily A Cordes, Matthew HJ Binford, Greta J Gillespie, Rosemary G https://orcid.org/0000-0003-0086-7424 Brewer, Michael S https://escholarship.org/uc/item/7dx3m9sj Amplicon based metabarcoding promises rapid and cost-efficient analyses of species composition. However, it is disputed whether abundance estimates can be derived from metabarcoding due to taxon specific PCR amplification biases. PCR-free approaches have been suggested to mitigate this problem, but come with considerable increases in workload and cost. Here, we analyze multilocus datasets of diverse arthropod communities, to evaluate whether amplification bias can be countered by (1) targeting loci with highly degenerate primers or conserved priming sites, (2) increasing PCR template concentration, (3) reducing PCR cycle number or (4) avoiding locus specific amplification by directly sequencing genomic DNA. Amplification bias is reduced considerably by degenerate primers or targeting amplicons with conserved priming sites. Surprisingly, a reduction of PCR cycles did not have a strong effect on amplification bias. The association of taxon abundance and read count was actually less... https://escholarship.org/uc/item/7dx3m9sj Thu, 17 Aug 2023 00:00:00 +0000 Krehenwinkel, Henrik Wolf, Madeline Lim, Jun Ying Rominger, Andrew J Simison, Warren B Gillespie, Rosemary G https://orcid.org/0000-0003-0086-7424 https://escholarship.org/uc/item/6jh609r8 Remote island archipelagos offer superb opportunities to study the evolution of community assembly because of their relatively young and simple communities where speciation contributes to the origin and evolution of community structure. There is great potential for common phylogeographic patterns among remote archipelagos that originate through hotspot volcanism, particularly when the islands formed are spatially isolated and linearly arranged. The progression rule is characterized by a phylogeographic concordance between island age and lineage age in a species radiation. Progression is most likely to arise when a species radiation begins on an older island before the emergence of younger islands of a hotspot archipelago. In the simplest form of progression, colonization of younger islands as they emerge and offer appropriate habitat, is coincident with cladogenesis. In this paper, we review recent discoveries of the progression rule on seven hotspot archipelagos. We then discuss... https://escholarship.org/uc/item/6jh609r8 Thu, 17 Aug 2023 00:00:00 +0000 Shaw, Kerry L Gillespie, Rosemary G https://orcid.org/0000-0003-0086-7424 https://escholarship.org/uc/item/6dq5w3s2 Spiders (Araneae) have a diverse spectrum of morphologies, behaviors, and physiologies. Attempts to understand the genomic-basis of this diversity are often hindered by their large, heterozygous, and AT-rich genomes with high repeat content resulting in highly fragmented, poor-quality assemblies. As a result, the key attributes of spider genomes, including gene family evolution, repeat content, and gene function, remain poorly understood. Here, we used Illumina and Dovetail Chicago technologies to sequence the genome of the long-jawed spider Tetragnatha kauaiensis, producing an assembly distributed along 3,925 scaffolds with an N50 of ∼2 Mb. Using comparative genomics tools, we explore genome evolution across available spider assemblies. Our findings suggest that the previously reported and vast genome size variation in spiders is linked to the different representation and number of transposable elements. Using statistical tools to uncover gene-family level evolution, we find... https://escholarship.org/uc/item/6dq5w3s2 Thu, 17 Aug 2023 00:00:00 +0000 Cerca, José Armstrong, Ellie E https://orcid.org/0000-0001-7107-6318 Vizueta, Joel Fernández, Rosa Dimitrov, Dimitar Petersen, Bent Prost, Stefan Rozas, Julio Petrov, Dmitri Gillespie, Rosemary G https://orcid.org/0000-0003-0086-7424 https://escholarship.org/uc/item/5vt4p4mq Biodiversity accumulates hierarchically by means of ecological and evolutionary processes and feedbacks. Within ecological communities drift, dispersal, speciation, and selection operate simultaneously to shape patterns of biodiversity. Reconciling the relative importance of these is hindered by current models and inference methods, which tend to focus on a subset of processes and their resulting predictions. Here we introduce massive ecoevolutionary synthesis simulations (MESS), a unified mechanistic model of community assembly, rooted in classic island biogeography theory, which makes temporally explicit joint predictions across three biodiversity data axes: (i) species richness and abundances, (ii) population genetic diversities, and (iii) trait variation in a phylogenetic context. Using simulations we demonstrate that each data axis captures information at different timescales, and that integrating these axes enables discriminating among previously unidentifiable community... https://escholarship.org/uc/item/5vt4p4mq Thu, 17 Aug 2023 00:00:00 +0000 Overcast, Isaac Ruffley, Megan Rosindell, James Harmon, Luke Borges, Paulo AV Emerson, Brent C Etienne, Rampal S Gillespie, Rosemary https://orcid.org/0000-0003-0086-7424 Krehenwinkel, Henrik Mahler, D Luke Massol, Francois Parent, Christine E Patiño, Jairo Peter, Ben Week, Bob Wagner, Catherine Hickerson, Michael J Rominger, Andrew https://escholarship.org/uc/item/50g0w58v The degree of similarity between the microbiotas of host species often mirrors the phylogenetic proximity of the hosts. This pattern, referred to as phylosymbiosis, is widespread in animals and plants. While phylosymbiosis was initially interpreted as the signal of symbiotic transmission and coevolution between microbes and their hosts, it is now recognized that similar patterns can emerge even if the microbes are environmentally acquired. Distinguishing between these two scenarios, however, remains challenging. We recently developed HOME (host-microbiota evolution), a cophylogenetic model designed to detect vertically transmitted microbes and host switches from amplicon sequencing data. Here, we applied HOME to the microbiotas of Hawaiian spiders of the genus <i>Ariamnes</i>, which experienced a recent radiation on the archipelago. We demonstrate that although Hawaiian <i>Ariamnes</i> spiders display a significant phylosymbiosis, there is little evidence of microbial vertical... https://escholarship.org/uc/item/50g0w58v Thu, 17 Aug 2023 00:00:00 +0000 Perez-Lamarque, Benoît Krehenwinkel, Henrik Gillespie, Rosemary G https://orcid.org/0000-0003-0086-7424 Morlon, Hélène https://escholarship.org/uc/item/4w4339d2 The interactions between insects and their plant host have been implicated in driving diversification of both players. Early arguments highlighted the role of ecological opportunity, with the idea that insects "escape and radiate" on new hosts, with subsequent hypotheses focusing on the interplay between host shifting and host tracking, coupled with isolation and fusion, in generating diversity. Because it is rarely possible to capture the initial stages of diversification, it is particularly difficult to ascertain the relative roles of geographic isolation versus host shifts in initiating the process. The current study examines genetic diversity between populations and hosts within a single species of endemic Hawaiian planthopper, Nesosydne umbratica (Hemiptera, Delphacidae). Given that the species was known as a host generalist occupying unrelated hosts, Clermontia (Campanulaceae) and Pipturus (Urticaceae), we set out to determine the relative importance of geography and host... https://escholarship.org/uc/item/4w4339d2 Thu, 17 Aug 2023 00:00:00 +0000 Goodman, Kari Roesch Prost, Stefan Bi, Ke Brewer, Michael S Gillespie, Rosemary G https://orcid.org/0000-0003-0086-7424 https://escholarship.org/uc/item/3mj32737 BACKGROUND: In light of the current biodiversity crisis, DNA barcoding is developing into an essential tool to quantify state shifts in global ecosystems. Current barcoding protocols often rely on short amplicon sequences, which yield accurate identification of biological entities in a community but provide limited phylogenetic resolution across broad taxonomic scales. However, the phylogenetic structure of communities is an essential component of biodiversity. Consequently, a barcoding approach is required that unites robust taxonomic assignment power and high phylogenetic utility. A possible solution is offered by sequencing long ribosomal DNA (rDNA) amplicons on the MinION platform (Oxford Nanopore Technologies). FINDINGS: Using a dataset of various animal and plant species, with a focus on arthropods, we assemble a pipeline for long rDNA barcode analysis and introduce a new software (MiniBar) to demultiplex dual indexed Nanopore reads. We find excellent phylogenetic and taxonomic... https://escholarship.org/uc/item/3mj32737 Thu, 17 Aug 2023 00:00:00 +0000 Krehenwinkel, Henrik Pomerantz, Aaron Henderson, James B Kennedy, Susan R Lim, Jun Ying Swamy, Varun Shoobridge, Juan Diego Graham, Natalie Patel, Nipam H Gillespie, Rosemary G https://orcid.org/0000-0003-0086-7424 Prost, Stefan https://escholarship.org/uc/item/3k78c6mb PCR amplification bias is a well-known problem in metagenomic analysis of arthropod communities. In contrast, variation of DNA degradation rates is a largely neglected source of bias. Differential degradation of DNA molecules could cause underrepresentation of taxa in a community sequencing sample. Arthropods are often collected by passive sampling devices, like malaise traps. Specimens in such a trap are exposed to varying periods of suboptimal storage and possibly different rates of DNA degradation. Degradation bias could thus be a significant issue, skewing diversity estimates. Here, we estimate the effect of differential DNA degradation on the recovery of community diversity of Hawaiian arthropods and their associated microbiota. We use a simple DNA size selection protocol to test for degradation bias in mock communities, as well as passively collected samples from actual Malaise traps. We compare the effect of DNA degradation to that of varying PCR conditions, including primer... https://escholarship.org/uc/item/3k78c6mb Thu, 17 Aug 2023 00:00:00 +0000 Krehenwinkel, Henrik Fong, Marisa Kennedy, Susan Huang, Edward Greg Noriyuki, Suzuki Cayetano, Luis Gillespie, Rosemary https://orcid.org/0000-0003-0086-7424 https://escholarship.org/uc/item/0ft3m5gz The deserts of southwestern North America have undergone dramatic changes over their recent geological history including large changes in size and connectivity during the Pleistocene glaciopluvial cycles. This study examines the population history of the rare spider Saltonia incerta, once thought to be extinct, to determine the role of past climatological events in shaping the structure of the species. This species is restricted to salt crusts of intermittent or dry lakes, streams or rivers in the desert southwest, a region that was much wetter during glacial periods. We examine the distribution and genetic variability of populations to test whether there is recent dispersal throughout the range of the species. Analyses of mitochondrial and nuclear DNA indicate significant population structure, with one major clade comprising New Mexico localities and one comprising California-northern Baja California localities. Finer-scale structure is evident within the California clade, although... https://escholarship.org/uc/item/0ft3m5gz Thu, 17 Aug 2023 00:00:00 +0000 Crews, Sarah C Gillespie, Rosemary G https://orcid.org/0000-0003-0086-7424 https://escholarship.org/uc/item/6z64d9qp Climate-driven changes in hydrological regimes are of global importance and are particularly significant in riparian ecosystems. Riparian ecosystems in California provide refuge to many native and vulnerable species within a xeric landscape. California Tetragnatha spiders play a key role in riparian ecosystems, serving as a link between terrestrial and aquatic elements. Their tight reliance on water paired with the widespread distributions of many species make them ideal candidates to better understand the relative role of waterways versus geographic distance in shaping the population structure of riparian species. To assist in better understanding population structure, we constructed a reference genome assembly for Tetragnatha versicolor using long-read sequencing, scaffolded with proximity ligation Omni-C data. The near-chromosome-level assembly is comprised of 174 scaffolds spanning 1.06 Gb pairs, with a scaffold N50 of 64.1 Mb pairs and BUSCO completeness of 97.6%. This reference... https://escholarship.org/uc/item/6z64d9qp Mon, 17 Jul 2023 00:00:00 +0000 Adams, Seira A https://orcid.org/0000-0003-1882-2806 Graham, Natalie R Holmquist, Anna J Sheffer, Monica M https://orcid.org/0000-0002-6527-4198 Steigerwald, Emma C https://orcid.org/0000-0003-1027-1421 Sahasrabudhe, Ruta Nguyen, Oanh Beraut, Eric Fairbairn, Colin Sacco, Samuel Seligmann, William https://orcid.org/0000-0002-5762-3095 Escalona, Merly https://orcid.org/0000-0003-0213-4777 Shaffer, H Bradley Toffelmier, Erin https://orcid.org/0000-0001-6028-8497 Gillespie, Rosemary G https://orcid.org/0000-0003-0086-7424