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1. Colour polymorphism and conspicuousness do not increase speciation rates in Lacertids

Author

de Solan, Thomas, Sinervo, Barry, Geniez, Philippe, David, Patrice, and Crochet, Pierre-André

Subjects
colouration, sexual selection, polymorphism, speciation, reptiles, Archaeology, CC1-960, Science
Abstract

Conspicuous body colours and colour polymorphism have been hypothesized to increase rates of speciation. Conspicuous colours are evolutionary labile, and often involved in intraspecific sexual signalling and thus may provide a raw material from which reproductive isolation can easily evolve, while polymorphism could favour rapid evolution of new lineages through morphic speciation. Here, we investigated the influence of the presence/absence of conspicuous colourations, and of colour polymorphism on the speciation of Lacertids. We used several state-dependent diversification models, and showed that, regardless of the methods, conspicuous colourations and colour polymorphism were not related to species speciation. While the lack of correlation between conspicuous colourations and speciation rates is in line with most of the literature testing this hypothesis, the results for colour polymorphism contradict previous studies, and question the generality of the morphic speciation hypothesis.

Published
2023
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4. Climate change and collapsing thermal niches of desert reptiles and amphibians: Assisted migration and acclimation rescue from extirpation

Author

Sinervo, Barry, Lara Reséndiz, Rafael A., Miles, Donald B., Lovich, Jeffrey E., Rosen, Philip C., Gadsden, Héctor, Gaytán, Gamaliel Casteñada, Tessaro, Patricia Galina, Luja, Víctor H., Huey, Raymond B., Whipple, Amy, Cordero, Víctor Sánchez, Rohr, Jason B., Caetano, Gabriel, Santos, Juan C., Sites, Jack W., Jr., and Méndez de la Cruz, Fausto R.

Published
2024
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6. Relaxed predation selection on rare morphs of Ensatina salamanders (Caudata: Plethodontidae) promotes a polymorphic population in a novel dune sand habitat

Author

Rich, Caitlyn, Reilly, Sean B, and Sinervo, Barry

Subjects
Biological Sciences, Evolutionary Biology
Abstract

Abstract The ring species Ensatina represents a classic example of locally adapted lineages. The Monterey ensatina (Ensatina eschscholtzii eschscholtzii) is a cryptic subspecies with brown coloration, although a recently discovered polymorphic population within a wind-blown sand region also contains leucistic (pink) and xanthistic (orange) morphs. In the present study, the frequency of leucism/xanthism was mapped across the subspecies’ range, revealing that these morphs are generally rare or absent except within regions containing light-coloured substrate. Attack rates were estimated using clay models of the three morphs, deployed only at the crepuscular period and during the night, on both light and dark substrates at a site within the dune sand region. Model selection found that the interaction between morph and substrate colour best predicted attack rates. Typical morphs had equal attack rates on both substrates while xanthistic and leucistic morphs incurred significantly fewer attacks on light vs. dark substrate, and there was no significant difference in attack rates among morphs on light substrates. These results support the idea that xanthistic and leucistic morphs are poorly adapted for dark substrates compared to typical morphs, but they are more or less equally adapted for light substrates. We suggest that this microgeographic island of relaxed selection on light-coloured morphs helps to explain the existence of this polymorphic population.

Published
2021

7. Cooling requirements fueled the collapse of a desert bird community from climate change

Author

Riddell, Eric A, Iknayan, Kelly J, Wolf, Blair O, Sinervo, Barry, and Beissinger, Steven R

Subjects
Climate Change Impacts and Adaptation, Biological Sciences, Ecology, Environmental Sciences, Climate Action, Animals, Basal Metabolism, Birds, Body Size, Body Temperature, Body Temperature Regulation, Climate Change, Desert Climate, Extinction, Biological, United States, Water, thermoregulation, climate change, desert birds, evaporative cooling, Bergmann's rule, Bergmann’s rule
Abstract

Climate change threatens global biodiversity by increasing extinction risk, yet few studies have uncovered a physiological basis of climate-driven species declines. Maintaining a stable body temperature is a fundamental requirement for homeothermic animals, and water is a vital resource that facilitates thermoregulation through evaporative cooling, especially in hot environments. Here, we explore the potential for thermoregulatory costs to underlie the community collapse of birds in the Mojave Desert over the past century in response to climate change. The probability of persistence was lowest for species occupying the warmest and driest sites, which imposed the greatest cooling costs. We developed a general model of heat flux to evaluate whether water requirements for evaporative cooling contributed to species' declines by simulating thermoregulatory costs in the Mojave Desert for 50 bird species representing the range of observed declines. Bird species' declines were positively associated with climate-driven increases in water requirements for evaporative cooling and exacerbated by large body size, especially for species with animal-based diets. Species exhibiting reductions in body size across their range saved up to 14% in cooling costs and experienced less decline than species without size reductions, suggesting total cooling costs as a mechanism underlying Bergmann's rule. Reductions in body size, however, are unlikely to offset the 50 to 78% increase in cooling costs threatening desert birds from future climate change. As climate change spreads warm, dry conditions across the planet, water requirements are increasingly likely to drive population declines, providing a physiological basis for climate-driven extinctions.

Published
2019

9. Integration of Genotype, Physiological Performance, and Survival in a Lizard (Uta stansburiana) with Alternative Mating Strategies.

Author

Hazard, Lisa C, Nagy, Kenneth A, Miles, Donald B, Svensson, Erik I, Costa, Daniel, and Sinervo, Barry

Subjects
Zoology, Ecology, Biological Sciences, Animals, Female, Genetic Fitness, Genotype, Lizards, Male, Selection, Genetic, Sexual Behavior, Animal, Species Specificity, alternative mating strategies, field metabolic rate, stamina, growth rate, Uta stansburiana, survivorship, Physiology, Medical Physiology, Ornithology, Biochemistry and cell biology, Medical physiology
Abstract

Covariation among behavioral and physiological traits is thought to enhance reproductive success and Darwinian fitness. Species that exhibit alternative mating strategies provide excellent opportunities to assess the relative contributions of physiological and behavioral traits to fitness. Male side-blotched lizards (Uta stansburiana) exhibit three heritable throat color morphs that are associated with alternative mating behaviors. The three morphs differ in resource holding potential, mate attraction, mate defense, and physiological performance. We examined interrelationships of body mass, stamina, field metabolic rate, growth rate, and survival to the second capture (a fitness proxy). Relationships among variables were complex, and mass, stamina, and throat color interacted to predict male survival. Our analyses suggest that male side-blotched lizards exhibit trade-offs among physiological traits related to reproductive success and survival and that differential survival for different combinations of traits has caused correlational selection, leading to adaptive integration of phenotypic traits associated with alternative mating strategies.

Published
2019

10. Habitat restoration opportunities, climatic niche contraction, and conservation biogeography in California's San Joaquin Desert

Author

Stewart, Joseph AE, Butterfield, H Scott, Richmond, Jonathan Q, Germano, David J, Westphal, Michael F, Tennant, Erin N, and Sinervo, Barry

Subjects
Environmental Sciences, Biological Sciences, Environmental Management, Life on Land, Climate Action, Agriculture, Animals, California, Climate Change, Conservation of Natural Resources, Desert Climate, Ecosystem, Endangered Species, Lizards, Models, Biological, Natural Resources, Phylogeography, General Science & Technology
Abstract

A recent global trend toward retirement of farmland presents opportunities to reclaim habitat for threatened and endangered species. We examine habitat restoration opportunities in one of the world's most converted landscapes, California's San Joaquin Desert (SJD). Despite the presence of 35 threatened and endangered species, agricultural expansion continues to drive habitat loss in the SJD, even as marginal farmland is retired. Over the next decades a combination of factors, including salinization, climate change, and historical groundwater overdraft, are projected to lead to the retirement of more than 2,000 km2 of farmland in the SJD. To promote strategic habitat protection and restoration, we conducted a quantitative assessment of habitat loss and fragmentation, habitat suitability, climatic niche stability, climate change impacts, habitat protection, and reintroduction opportunities for an umbrella species of the SJD, the endangered blunt-nosed leopard lizard (Gambelia sila). We use our suitability models, in conjunction with modern and historical land use maps, to estimate the historical and modern rate of habitat loss to development. The estimated amount of habitat lost since the species became protected under endangered species law in 1967 is greater than the total amount of habitat currently protected through public ownership and conservation easement. We document climatic niche contraction and associated range contraction away from the more mesic margins of the species' historical distribution, driven by the anthropogenic introduction of exotic grasses and forbs. The impact of exotic species on G. sila range dynamics appears to be still unfolding. Finally, we use NASA fallowed area maps to identify 610 km2 of fallowed or retired agricultural land with high potential to again serve as habitat. We discuss conservation strategies in light of the potential for habitat restoration and multiple drivers of ongoing and historical habitat loss.

Published
2019

11. The Genetic Basis of Adaptation following Plastic Changes in Coloration in a Novel Environment

Author

Corl, Ammon, Bi, Ke, Luke, Claudia, Challa, Akshara Sree, Stern, Aaron James, Sinervo, Barry, and Nielsen, Rasmus

Subjects
Biological Sciences, Ecology, Genetics, Aetiology, 2.1 Biological and endogenous factors, Adaptation, Physiological, Animals, California, Color, Environment, Lizards, Melanins, Phenotype, Pigmentation, Reptilian Proteins, Baldwin effect, PREP gene, PRKAR1A gene, Uta stansburiana, adaptation, crypsis, exon-capture, lizard, melanin, plasticity, Medical and Health Sciences, Psychology and Cognitive Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences, Psychology
Abstract

Phenotypic plasticity has been hypothesized to precede and facilitate adaptation to novel environments [1-8], but examples of plasticity preceding adaptation in wild populations are rare (but see [9, 10]). We studied a population of side-blotched lizards, Uta stansburiana, living on a lava flow that formed 22,500 years ago [11] to understand the origin of their novel melanic phenotype that makes them cryptic on the black lava. We found that lizards living on and off of the lava flow exhibited phenotypic plasticity in coloration but also appeared to have heritable differences in pigmentation. We sequenced the exomes of 104 individuals and identified two known regulators of melanin production, PREP and PRKAR1A, which had markedly increased levels of divergence between lizards living on and off the lava flow. The derived variants in PREP and PRKAR1A were only found in the lava population and were associated with increased pigmentation levels in an experimental cohort of hatchling lizards. Simulations suggest that the derived variants in the PREP and PRKAR1A genes arose recently and were under strong positive selection in the lava population. Overall, our results suggest that ancestral plasticity for coloration facilitated initial survival in the lava environment and was followed by genetic changes that modified the phenotype in the direction of the induced plastic response, possibly through de novo mutations. These observations provide a detailed example supporting the hypothesis that plasticity aids in the initial colonization of a novel habitat, with natural selection subsequently refining the phenotype with genetic adaptations to the new environment. VIDEO ABSTRACT.

Published
2018

12. Harnessing cross-border resources to confront climate change

Author

Aburto-Oropeza, Octavio, Johnson, Andrew F, Agha, Mickey, Allen, Edith B, Allen, Michael F, González, Jesús Arellano, Moreno, Diego M Arenas, Beas-Luna, Rodrigo, Butterfield, Scott, Caetano, Gabriel, Caselle, Jennifer E, Gaytán, Gamaliel Castañeda, Castorani, Max CN, Cat, Linh Anh, Cavanaugh, Kyle, Chambers, Jeffrey Q, Cooper, Robert D, Arafeh-Dalmau, Nur, Dawson, Todd, de la Vega Pérez, Aníbal Díaz, DiMento, Joseph FC, Guerrero, Saúl Domínguez, Edwards, Matthew, Ennen, Joshua R, Estrada-Medina, Hector, Fierro-Estrada, Natalia, Gadsden, Héctor, Galina-Tessaro, Patricia, Gibbons, Paul M, Goode, Eric V, Gorris, Morgan E, Harmon, Thomas, Hecht, Susanna, Fragoso, Marco Antonio Heredia, Hernández-Solano, Alan, Hernández-Cortés, Danae, Hernández-Carmona, Gustavo, Hillard, Scott, Huey, Raymond B, Hufford, Matthew B, Jenerette, G Darrel, Jiménez-Osornio, Juan, López-Nava, Karla Joana, Reséndiz, Rafael A Lara, Leslie, Heather M, López-Feldman, Alejandro, Luja, Víctor H, Méndez, Norberto Martínez, Mautz, William J, Medellín-Azuara, Josué, Meléndez-Torres, Cristina, de la Cruz, Fausto R Méndez, Micheli, Fiorenza, Miles, Donald B, Montagner, Giovanna, Montaño-Moctezuma, Gabriela, Müller, Johannes, Oliva, Paulina, Álvarez, José Abraham Ortinez, Ortiz-Partida, J Pablo, Palleiro-Nayar, Julio, Figueroa, Víctor Hugo Páramo, Parnell, P Ed, Raimondi, Peter, Ramírez-Valdez, Arturo, Randerson, James T, Reed, Daniel C, Riquelme, Meritxell, Torres, Teresita Romero, Rosen, Philip C, Ross-Ibarra, Jeffrey, Sánchez-Cordero, Victor, Sandoval-Solis, Samuel, Santos, Juan Carlos, Sawers, Ruairidh, Sinervo, Barry, Sites, Jack W, Sosa-Nishizaki, Oscar, Stanton, Travis, Stapp, Jared R, Stewart, Joseph AE, Torre, Jorge, Torres-Moye, Guillermo, Treseder, Kathleen K, Valdez-Villavicencio, Jorge, Jiménez, Fernando I Valle, Vaughn, Mercy, Welton, Luke, Westphal, Michael F, Woolrich-Piña, Guillermo, Yunez-Naude, Antonio, Zertuche-González, José A, and Taylor, J Edward

Subjects
Environmental Sciences, Political Science, Human Society, Climate Action, US southwest, Northern Mexico, Binational collaborations, Environmental innovation, Cross-border transformation, Research integration, Agricultural and Veterinary Sciences, Studies in Human Society, Agricultural, veterinary and food sciences, Environmental sciences, Human society
Abstract

The US and Mexico share a common history in many areas, including language and culture. They face ecological changes due to the increased frequency and severity of droughts and rising energy demands; trends that entail economic costs for both nations and major implications for human wellbeing. We describe an ongoing effort by the Environment Working Group (EWG), created by The University of California's UC-Mexico initiative in 2015, to promote binational research, teaching, and outreach collaborations on the implications of climate change for Mexico and California. We synthesize current knowledge about the most pressing issues related to climate change in the US-Mexico border region and provide examples of cross-border discoveries and research initiatives, highlighting the need to move forward in six broad rubrics. This and similar binational cooperation efforts can lead to improved living standards, generate a collaborative mindset among participating universities, and create an international network to address urgent sustainability challenges affecting both countries.

Published
2018

13. Behavioral and physiological polymorphism in males of the austral lizard Liolaemus sarmientoi

Author

Fernández, Jimena B, Bastiaans, Elizabeth, Medina, Marlin, Méndez De la Cruz, Fausto R, Sinervo, Barry R, and Ibargüengoytía, Nora R

Subjects
Zoology, Ecology, Biological Sciences, Behavioral and Social Science, Aggression, Animals, Behavior, Animal, Body Temperature, Head, Lizards, Male, Movement, Organ Size, Physical Endurance, Pigmentation, Agonistic behavior, Color morph, Locomotor stamina, Morphology, Thermal physiology, Medical and Health Sciences, Neurology & Neurosurgery, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Integrative behavioral studies show that the interplay between individual physiology and social behavior influences the ecology of the species, ultimately affecting individual fitness. Particularly in lizards, color polymorphism is associated with differential behaviors and reproductive strategies, which are evident in mature males during the mating season. Dominant males generally have greater endurance, higher body temperature, and larger bodies than submissive males, so they can acquire and defend larger territories and have greater access to females for mating. We studied whether the color morphs observed in males of one of the world's southernmost reptiles, Liolaemus sarmientoi, are related to behavioral variation during agonistic interactions, thermal physiology, morphology, and/or locomotor stamina. Liolaemus sarmientoi males exhibit three color morphs: red (RR), red-yellow (RY), and yellow (YY). These lizards exhibit subtle behavioral displays and we did not observe stamina differences among morphs. However, we found that RR males are more aggressive than YY males during agonistic encounters. In addition, greater body temperature change during trials, higher field body temperatures, and greater head sizes of RR males compared to RY or YY indicate that RR is a dominant morph, which may influence their ability to acquire and defend territory and tactics for achieving reproductive success.

Published
2018

16. Climate Change and Collapsing Thermal Niches of Mexican Endemic Reptiles 

Author

Sinervo, Barry, Lara Reséndiz, Rafael A, Miles, Donald B, Lovich, Jeffrey E, Ennen, Joshua R, Müller, Johannes, Cooper, Robert D, Rosen, Philip C, Stewart, Joseph A. E, Santos, Juan Carlos, Sites Jr., Jack W, Gibbons, Paul M, Goode, Eric V, Hillard, L. Scott, Welton, Luke, Agha, Mickey, Caetano, Gabriel, Vaughn, Mercy, Meléndez Torres, Cristina, Gadsden, Héctor, Casteñada Gaytán, Gamaliel, Galina Tessaro, Patricia, Valle Jiménez, Fernando I, Valdez Villavicencio, Jorge, Martínez Méndez, Norberto, Piña, Guillermo W, Luja Molina, Victor, Díaz de la Vega Pérez, Aníbal, Arenas Moreno, Diego M, Dominguez Guerrero, Saúl, Fierro, Natalia, Butterfield, Scott, Westph, Michael, Huey, Raymond B, Mautz, William, Sánchez Cordero, Víctor, and Méndez de la Cruz, Fausto R

Published
2017

17. Contemporary Drought and Future Effects of Climate Change on the Endangered Blunt-Nosed Leopard Lizard, Gambelia sila

Author

Westphal, Michael F, Stewart, Joseph AE, Tennant, Erin N, Butterfield, H Scott, and Sinervo, Barry

Subjects
Climate Change Impacts and Adaptation, Biological Sciences, Ecology, Zoology, Environmental Sciences, Climate Action, Life on Land, Animals, Climate Change, Droughts, Endangered Species, Lizards, Population Dynamics, Weather, General Science & Technology
Abstract

Extreme weather events can provide unique opportunities for testing models that predict the effect of climate change. Droughts of increasing severity have been predicted under numerous models, thus contemporary droughts may allow us to test these models prior to the onset of the more extreme effects predicted with a changing climate. In the third year of an ongoing severe drought, surveys failed to detect neonate endangered blunt-nosed leopard lizards in a subset of previously surveyed populations where we expected to see them. By conducting surveys at a large number of sites across the range of the species over a short time span, we were able to establish a strong positive correlation between winter precipitation and the presence of neonate leopard lizards over geographic space. Our results are consistent with those of numerous longitudinal studies and are in accordance with predictive climate change models. We suggest that scientists can take immediate advantage of droughts while they are still in progress to test patterns of occurrence in other drought-sensitive species and thus provide for more robust models of climate change effects on biodiversity.

Published
2016

18. Climate change and collapsing thermal niches of desert reptiles and amphibians: Assisted migration and acclimation rescue from extirpation

Author

Sinervo, Barry, primary, Lara Reséndiz, Rafael A., additional, Miles, Donald B., additional, Lovich, Jeffrey E., additional, Rosen, Philip C., additional, Gadsden, Héctor, additional, Gaytán, Gamaliel Casteñada, additional, Tessaro, Patricia Galina, additional, Luja, Víctor H., additional, Huey, Raymond B., additional, Whipple, Amy, additional, Cordero, Víctor Sánchez, additional, Rohr, Jason B., additional, Caetano, Gabriel, additional, Santos, Juan C., additional, Sites, Jack W., additional, and Méndez de la Cruz, Fausto R., additional

Published
2023
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19. Quantum Structure in Competing Lizard Communities

Author

Aerts, Diederik, Broekaert, Jan, Czachor, Marek, Kuna, Maciej, Sinervo, Barry, and Sozzo, Sandro

Subjects
Physics - Biological Physics, Quantitative Biology - Populations and Evolution, Quantum Physics
Abstract

Almost two decades of research on applications of the mathematical formalism of quantum theory as a modeling tool in domains different from the micro-world has given rise to many successful applications in situations related to human behavior and thought, more specifically in cognitive processes of decision-making and the ways concepts are combined into sentences. In this article, we extend this approach to animal behavior, showing that an analysis of an interactive situation involving a mating competition between certain lizard morphs allows to identify a quantum theoretic structure. More in particular, we show that when this lizard competition is analyzed structurally in the light of a compound entity consisting of subentities, the contextuality provided by the presence of an underlying rock-paper-scissors cyclic dynamics leads to a violation of Bell's inequality, which means it is of a non-classical type. We work out an explicit quantum-mechanical representation in Hilbert space for the lizard situation and show that it faithfully models a set of experimental data collected on three throat-colored morphs of a specific lizard species. Furthermore, we investigate the Hilbert space modeling, and show that the states describing the lizard competitions contain entanglement for each one of the considered confrontations of lizards with different competing strategies, which renders it no longer possible to interpret these states of the competing lizards as compositions of states of the individual lizards., Comment: 28 pages

Published
2012
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21. Female Preference for Sympatric vs. Allopatric Male Throat Color Morphs in the Mesquite Lizard (Sceloporus grammicus) Species Complex

Author

Bastiaans, Elizabeth, Bastiaans, Mary Jane, Morinaga, Gen, Castañeda Gaytán, José Gamaliel, Marshall, Jonathon C, Bane, Brendan, de la Cruz, Fausto Méndez, and Sinervo, Barry

Subjects
2 CHROMOSOME RACES, KEELED EARLESS LIZARDS, VISUAL MATE CHOICE, MALE TREE LIZARDS, SEXUAL SELECTION, CICHLID FISH, HYBRID ZONE, AGGRESSIVE-BEHAVIOR, UROSAURUS-ORNATUS, IGUANID LIZARD
Abstract

Color polymorphic sexual signals are often associated with alternative reproductive behaviors within populations, and the number, frequency, or type of morphs present often vary among populations. When these differences lead to assortative mating by population, the study of such polymorphic taxa may shed light on speciation mechanisms. We studied two populations of a lizard with polymorphic throat color, an important sexual signal. Males in one population exhibit orange, yellow, or blue throats; whereas males in the other exhibit orange, yellow, or white throats. We assessed female behavior when choosing between allopatric and sympatric males. We asked whether females discriminated more when the allopatric male was of an unfamiliar morph than when the allopatric male was similar in coloration to the sympatric male. We found that female rejection of allopatric males relative to sympatric males was more pronounced when males in a pair were more different in throat color. Our findings may help illuminate how behavioral responses to color morph differences between populations with polymorphic sexual signals contribute to reproductive isolation.

Published
2014

22. Natural parasites in conjunction with behavioral and color traits explain male agonistic behaviors in a lizard.

Author

Megía-Palma, Rodrigo, Paranjpe, Dhanashree, Cooper, Robert D, Blaimont, Pauline, and Sinervo, Barry

Subjects
LIZARDS, PARASITIC diseases, MALES, COCCIDIA, AGGRESSION (Psychology)
Abstract

Male competition conforms to a cost–benefit model, because while aggression may increase reproductive prospects, it can also increase the risk of injury. We hypothesize that an additional cost in aggressive males would be an increase in parasite load associated with a high energy investment into sexual competition. Some of these infections, in turn, may downmodulate the level of host aggression via energetic trade-offs. We staged dyadic male contests in the lab to investigate the relationships of multiple parasites with the agonistic behavior of lizard hosts, Sceloporus occidentalis. We also included both color and behavioral traits from opponents in the analyses because (1) color patches of lizards may serve as intraspecific signals used by conspecifics to assess the quality of opponents, and (2) contests between male lizards fit classical models of escalated aggression, where lizards increase aggression displays in response to an opponent's behavior. The results conform to our hypothesis because male lizards displayed more pushups when they had more ticks. Moreover, some parasites may modulate the levels of aggression because lizards infected by hematic coccidians performed fewer pushups. Interestingly, lizards also displayed fewer pushups when both the chroma and size of the opponent's blue patch were greater. The results thus also supported the role of the blue patch of S. occidentalis as a sexual armament, because it contributed to the deterrence of aggression from opponent lizards. We revealed that natural parasitic infections in lizard hosts can contribute to their agonistic behavior. We encourage future studies to account for parasites in behavioral tests with lizards. [ABSTRACT FROM AUTHOR]

Published
2024
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25. Climate Change and Extinctions

Author

Sinervo, Barry

Subjects
Climate Change
Abstract

The UCSC University Library Synergy Lecture Series is excited to welcome Distinguished Professor Dr. Barry Sinervo as our Synergy Lecturer for Spring 2013.  He will present a climate change extinction model that has been validated by known lizard extinctions, and explain how this model can be extended to other vertebrates.Presented April 24, 2013, 3-4pm in the  Ching-Yi Dougherty Reading Room of the UCSC Science & Engineering Library.

Published
2013

41. Data and code from: Plastic responses to warmer climates: a semi-natural experiment on lizard populations

Author

Bestion, Elvire, San-Jose, Luis M., Di Gesu, Lucie, Richard, Murielle, Sinervo, Barry, Côte, Jessica, Calvez, Olivier, Guillaume, Olivier, and Cote, Julien

Subjects
climate change, intergenerational plasticity, thermal physiology, natural selection, lizard, ectotherm, phenotypic plasticity
Abstract

GENERAL INFORMATION -------------------------------------------- 1. Title of Dataset: Data and code for: Plastic responses to warmer climates: a semi-natural experiment on lizard populations, Bestion et al 2023, Evolution doi: 10.1093/evolut/qpad070 2. Author Information A. First Author Contact Information Name: Elvire Bestion Institution: Station d’Ecologie Théorique et Expérimentale, CNRS, UAR 2029 Address: 2 route du CNRS, 09200 Moulis, France Email: elvire.bestion@sete.cnrs.fr B. Last Author Contact Information Name: Julien Cote Institution: Laboratoire Evolution et Diversité Biologique, CNRS, Université Toulouse III Paul Sabatier, UMR 5174 Address: 118 route de Narbonne, 31062 Toulouse, France Email: julien.cote@univ-tlse3.fr 3. Abstract: Facing warming environments, species can exhibit plastic or microevolutionary changes in their thermal physiology to adapt to novel climates. Here, using semi-natural mesocosms, we experimentally investigated over two successive years whether a 2°C-warmer climate produces selective and inter- and intragenerational plastic changes in the thermal traits (preferred temperature and dorsal colouration) of the lizard Zootoca vivipara. In a warmer climate, the dorsal darkness, dorsal contrast and preferred temperature of adults plastically decreased and covariances between these traits were disrupted. While selection gradients were overall weak, selection gradients for darkness were slightly different between climates and in the opposite direction to plastic changes. Contrary to adults, male juveniles were darker in warmer climates either through plasticity or selection and this effect was strengthened by intergenerational plasticity when juveniles’ mothers also experienced warmer climates. While the plastic changes in adult thermal traits alleviate the immediate overheating costs of warming, its opposite direction to selective gradients and to juveniles’ phenotypic responses may slow down evolutionary shifts towards phenotypes that are better adapted to future climates. Our study demonstrates the importance of considering inter- and intragenerational plasticity along with selective processes to better understand adaptation and population dynamics in light of climate change. 4. Keywords: climate change, ectotherm, lizard, phenotypic plasticity, natural selection, intergenerational plasticity, thermal physiology 5. Date of data collection: May 2012 to May 2014 for the main dataset, and May 2013 to May 2015 for the side-experiment on maternal effects 6. Geographic location of data collection: Station of Theoretical and Experimental Ecology, Ariège, France, 43°01' N, 1°05' E 7. Taxon/species from which data was collected: Common lizards (Zootoca vivipara, Jacquin 1787) SHARING/ACCESS INFORMATION --------------------------------------------------- 1. Licenses/restrictions placed on the data: The data is usable under Creative Commons Attribution 4.0 International licence but we would appreciate if we were contacted prior to meaningful use, and this dataset and the matching paper cited if appropriate. 2. Links to publications that cite or use the data: This dataset corresponds to the data used in: Bestion E, San-Jose LM, Di Gesu L, Richard M, Sinervo B, Côte J, Calvez O, Guillaume O, & Cote J. 2023. Plastic responses to warmer climates: a semi-natural experiment on lizard populations. Evolution, doi: 10.1093/evolut/qpad070 3. Links to other publicly accessible locations of the data: The data can be found on zenodo at doi:10.5281/zenodo.7845944 4. Was data derived from another source? NO 5. Recommended citation for this dataset: Bestion et al, 2023. Data and code from: Plastic responses to warmer climates: a semi-natural experiment on lizard populations. Evolution, Zenodo doi: 10.5281/zenodo.7845944 DATA & FILE OVERVIEW ------------------------------------- The data is composed of a zip file containing: * The present README.txt file * Nine R files used to run the analyses: # 0_important_functions.R --> functions used in the main analysis scripts # 1_climate_impact_on_phenotype_at_tp1.R --> the 1st part of the main R script. The script calls to the 0_important_functions.R for functions, uses data in the /data folder, outputs diagnostic plots and info in the /interm folder, outputs means and SEM for figures to the /figure_values folders. This first part of the analysis script tests for the impacts of climate warming on thermal phenotype at t+1 in the juveniles and adults from the main 2012-2013 experiment. # 2_plasticity.R --> The 2nd part of the main script, to be run after #1 script. This part of the analysis tests for plastic effects of climate warming on phenotype in juveniles and adults from the main 2012-2013 experiment. # 3_selection.R --> The 3rd part of the main script, to be run after #2 script. This part of the analysis tests for differential selection in phenotypic traits depending on climate in juveniles and adults from the main 2012-2013 experiment. # 4_heritability.R --> The 4th part of the main script, to be run after #3 script. This part of the analysis tests heritability of phenotypic traits in juveniles from the main 2012-2013 experiment. # 5_SEM.R --> The 5th part of the main script, to be run after #4 script. This part of the analysis tests for the impact of climate warming on thermal syndromes, i.e. covariation between thermal traits in juveniles and adults from the main 2012-2013 experiment. # 6_maternal_effects.R --> The 6th part of the main script, to be run after #5 script. This part of the analysis uses the data from juveniles in 2013 issued from surviving mothers from the 2012 experiment, supplemented with a side experiment in 2014 on the juveniles issued from surviving mothers from the 2013 experiment, to test for the impact of climate warming on intergenerational plasticity of thermal traits. # 7_checking_models_with_deltaAIC_4.R --> The 7th part of the main script, to be run after #6 script. This part checks for the of the analysis tests for the impact of climate warming on thermal syndromes, i.e. covariation between thermal traits in juveniles and adults from the main 2012-2013 experiment. # 8_exporting_tables_to_word.R --> The 8th part of the main script, to be run after all scripts. This part creates the composite figures and outputs them and the tables to the /out folder. * A /data folder with 3 datasets: # data/Bestion_adults.csv --> dataset for adults and yearlings from the main 2012-2013 experiment, to test the impacts of climate warming on phenotype at t+1, selection and plasticity on the traits. # data/Bestion_adults.csv --> dataset for juveniles from the main 2012-2013 experiment, to test the impacts of climate warming on phenotype at t+1, selection and plasticity on the traits, and heritability of the traits. # data/Bestion_juveniles_for_maternal_effects.csv --> dataset including juveniles in 2013 born from the mothers surviving the 2012 experiment, and including juveniles in a side-experiment in 2014 that were born from the mothers surviving the 2013 experiment, to test the impact of intergenerational plasticity. * An /interm folder with : # interm/R_session_info_2023-03-29.txt --> the session information about the R version and R packages used when running the R code # note that while running the R code, other data will be saved to the /interm folder (e.g. heritability models, diagnostic plots about all models, …). Only the files that cannot be reproduced by the R code alone such as the session info were kept in the folder for facility of use. * An empty /figure_values folder. While running the R code, data with the means and SEM of the traits by climates will be saved to the folder, to easily reproduce figures and get summarised data for meta-analyses. * An /out folder with the figures and tables resulting from the analysis and found in the main paper and the supplementary data: # out/Figure_2_traits_adults_tp1.png --> the figure 2 # out/Figure_3_plasticity_selection_adults.png--> the figure 3 # out/Figure_4_maternal_effects_juveniles.png --> the figure 4 # out/Figure_SB1_traits_juveniles_tp1.png --> the figure SB1 # out/Figure_SC1_selection_juveniles.png--> the figure SC1 # out/Figure_SD1_plasticity_juveniles.png--> the figure SD1 # out/Figure_SD2_impacts_of_plasticity_on_survival_adults.png--> the figure SD2 # out/Appendix B - Impact of climatic treatment on phenotype at tp1.docx --> The tables SB1 to SB4 from the appendix B, as well as information about the models from the tables to add to the legends of the tables (e.g. N, R²m and R²c, SD explained by random components, variance inflation factors for the variables in the models). # out/Appendix C - Selective processes.docx --> The tables SC1 to SC3 from the appendix C, as well as information about the models from the tables to add to the legends of the tables. # out/Appendix D - Trait plasticity.docx --> The tables SD1 to SD3 from the appendix D, as well as information about the models from the tables to add to the legends of the tables. # out/Appendix E - Heritability of phenotypic traits.docx -->The table SE1 from the appendix E. # out/Appendix F - Maternal effects.docx --> The table SF1 from the appendix F, as well as information about the models from the table to add to the legend of the table. # out/Appendix G - Robustness of statistical results.docx --> The tables SG1 to SG4 from the appendix G, as well as information about the models from the tables to add to the legends of the tables. METHODOLOGICAL INFORMATION -------------------------------------------------- 1. Description of methods used for collection/generation of data: A detailed explanation of the methods is provided in the related Bestion et al 2023 Evolution article, please refer to it for a full understanding of the methods and results. Briefly: Our aim was to study experimentally whether climate warming affected the thermal phenotype (i.e. preferred temperature, dorsal darkness, dorsal contrast) of a lizard through selection, intra-generational and inter-generational plasticity. Between May 2012 and May 2014, we performed two one-year experiments inside of the Metatron (Legrand et al. 2012, Nature Methods), a system of forty-eight 10 x 10 m semi-natural mesocosms. Over the two years of experiment, we created 16 populations in 16 mesocosms, and simulated present-day and +2°C warmer climatic conditions through the use of automatic shutters. Every year, mid-May, we captured all surviving lizards from the mesocosms. We measured them for body size, a tail tip was taken for paternity analysis, and a dorsal picture was taken to measure dorsal darkness and dorsal contrast. We assessed lizard preferred temperature in a thermal gradient. Female gave birth inside of the terraria, and juveniles were also genotyped for paternity analysis, measured for body size, and their preferred temperature was assessed. In June-July, lizards were released into the mesocosms to form 16 populations released into 3 mesocosms per climate (i.e. 6 mesocosms) in 2012, and 5 mesocosms per climate (i.e. 10 mesocosms) in 2013. . Each mesocosm contained 11 ± 1 two-or-more-year-old (2+yo) females, 6 ± 1 (2+yo) males, 9 ± 2 one-year-olds (1yo) and 37 ± 4 juveniles ( The data from the two years of experiment allowed to test 4 main questions: 1) What is the impact of a warmer climate on lizard thermal phenotype (studying traits at t+1 on survivors) and thermal syndromes between traits, 2) Is the impact due to plasticity (effect of climate on traits at t and t+1), 3) Is the impact due to selection (impacts of traits at t on survival at t+1), 4) Are the traits heritable? Further, the data from the 2013 experiment on juveniles, together with data from a side-experiment in 2014 also on juveniles maintained in the Metatron in the two climate treatments, allowed to test a 5th question: 5) what is the impact of inter- and intra-generational plasticity on thermal traits? 2. Instrument- or software-specific information needed to interpret the data: To reproduce the analyses, the data should be read in R with the provided R scripts. The R version and the version of the packages used to reproduce the data are found in the interm/ R_session_info_2023-03-29.txt file. 3. Environmental/experimental conditions: The experiment was done in 10 x 10 m semi-natural mesocosms, in which lizards were maintained for one year at a time. Two climatic treatments were applied to the mesocosms, a present-day climate and a +2°C warmer climate. 4. People involved with sample collection, processing, analysis and/or submission: Elvire Bestion and Julien Cote designed the study, Elvire Bestion, Lucie Di Gesu, Olivier Calvez, Olivier Guillaume and Julien Cote performed the experiment, Murielle Richard performed the extractions, the polymerase chain reaction and analysed the paternity data. Barry Sinervo, Jessica Côte and Luis M. San Jose provided assistance with the animal models. Elvire Bestion and Julien Cote analysed and interpreted the data. Elvire Bestion and Julien Cote wrote the first draft and Luis M. San Jose, Barry Sinervo, Murielle Richard and Jessica Côte significantly contributed to redrafting. 5. Ethics statement: Experiments followed French ethics regulations and CNRS institutional ethics guidelines. We applied the 3R rule by reducing the number of lizards to the minimum to form enough populations and providing care appropriate to the species. Lizards were captured from the wild according to the capture licence number 2010-189-16 DREAL and transferred to the laboratory (laboratory use of animals: agreement B09583). Experiments were started before the need of obtaining a permit following French law (article R.214-113, ordonnance 2012-10, décret 2013-118, arrêtés 1er février 2013, transposing EU directive 2010/63/UE), however we then obtained a permit for further experiments following the same procedure (permits number APAFIS#15897-2018070615164391 v3 and APAFIS#19523-201902281559649 v3 obtained from the ethics comity n°068). DATA-SPECIFIC INFORMATION ----------------------------------------------- DATA-SPECIFIC INFORMATION FOR: Bestion_adults.csv ----------------------------------------------- 1. Number of variables: 20 2. Number of cases/rows: 380 3. Variable List: Year: year of the experiment (2012 or 2013) Code: code of the individual (identification) Age_t: age of the individual at the time of the start of the experiment, as a class (A: adult: 2+ year-old, Y: yearling: 1 year-old) Sex: sex of the individual, M or F Body_size_t: body size at the start of the experiment, snout-vent length in mm Tpref_t: preferred temperature at the start of the experiment, in °C Dorsal_darkness_t: mean dorsal darkness at the start of the experiment, mean percentage of black pixels between the median part and the flanks Dorsal_contrast_t: dorsal contrast at the start of the experiment, as absoltue darkness difference between the flanks and median parts divided by median darkness Darkness_median_part_t: dorsal darkness in the median part of the lizard body at the start of the experiment, percentage of black pixels in transformed pictures Darkness_flanks_t: dorsal darkness in the flanks of the lizard at the start of the experiment, percentage of black pixels in transformed pictures Climate_Intro: Climatic treatment inside of the mesocosm, either warm or present Mesocosm_Intro: mesocosm number (identification) Population_Intro: composite identification number composed of the mesocosm number and the year (identification) Survival: survival after one year of experiment inside of the mesocosms, 1= survived or 0 = dead Body_size_tp1: body size at the end of the experiment on survivors, snout-vent length in mm Tpref_tp1: preferred temperature at the start of the experiment, in °C Dorsal_darkness_tp1: mean dorsal darkness at the end of the experiment on survivors, mean percentage of black pixels between the median part and the flanks Dorsal_contrast_tp1: dorsal contrast at the end of the experiment on survivors, as absolute darkness difference between the flanks and median parts divided by median darkness Darkness_median_part_tp1: dorsal darkness in the median part of the lizard at the end of the experiment on survivors, percentage of black pixels in transformed pictures Darkness_flanks_tp1: dorsal darkness in the flanks of the lizard at the end of the experiment on survivors, percentage of black pixels in transformed pictures 4. Missing data codes: NA (for traits at t+1 of individuals that did not survive to t+1, and rare missing measurements at t or t+1) DATA-SPECIFIC INFORMATION FOR: Bestion_juveniles.csv ----------------------------------------------- 1. Number of variables: 19 2. Number of cases/rows: 536 3. Variable List: Year: year of the experiment (2012 or 2013) Code: code of the individual (identification) Code_Mother: code of the mother of the individual (identification) Code_Father: code of the father of the individual (identification) Age_t

Published
2023
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45. Climate Change and Collapsing Thermal Niches of Desert Reptiles and Amphibians: Assisted Migration and Acclimation Rescue from Extirpation

Author

Miles, Donald B., primary, Sinervo, Barry, additional, Lara-Resendiz, Rafa, additional, Lovich, Jeff, additional, Rosen, Philip C., additional, Gadsden, Hector, additional, Castenada, Gamaliel, additional, Galina, Patricia, additional, Luja, Victor, additional, Huey, Raymond, additional, Whipple, Amy, additional, Sanchez, Victor, additional, Rohr, Jason, additional, Caetano, Gabriel, additional, Santos, Juan, additional, Sites Jr., Jack, additional, and Méndez de la Cruz, Fausto Roberto, additional

Published
2023
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50. Environmental temperatures shape thermal physiology as well as diversification and genome-wide substitution rates in lizards

Author

Garcia-Porta, Joan, Irisarri, Iker, Kirchner, Martin, Rodríguez, Ariel, Kirchhof, Sebastian, Brown, Jason L., MacLeod, Amy, Turner, Alexander P., Ahmadzadeh, Faraham, Albaladejo, Gonzalo, Crnobrnja-Isailovic, Jelka, De la Riva, Ignacio, Fawzi, Adnane, Galán, Pedro, Göçmen, Bayram, Harris, D. James, Jiménez-Robles, Octavio, Joger, Ulrich, Jovanović Glavaš, Olga, Karış, Mert, Koziel, Giannina, Künzel, Sven, Lyra, Mariana, Miles, Donald, Nogales, Manuel, Oğuz, Mehmet Anıl, Pafilis, Panayiotis, Rancilhac, Loïs, Rodríguez, Noemí, Rodríguez Concepción, Benza, Sanchez, Eugenia, Salvi, Daniele, Slimani, Tahar, S’khifa, Abderrahim, Qashqaei, Ali Turk, Žagar, Anamarija, Lemmon, Alan, Moriarty Lemmon, Emily, Carretero, Miguel Angel, Carranza, Salvador, Philippe, Hervé, Sinervo, Barry, Müller, Johannes, Vences, Miguel, and Wollenberg Valero, Katharina C.

Published
2019
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