Diversity of ageing across the tree of life.

Evolution drives, and is driven by, demography. A genotype moulds its phenotype's age patterns of mortality and fertility in an environment; these two patterns in turn determine the genotype's fitness in that environment. Hence, to understand the evolution of ageing, age patterns of mortality and reproduction need to be compared for species across the tree of life. However, few studies have done so and only for a limited range of taxa. Here we contrast standardized patterns over age for 11 mammals, 12 other vertebrates, 10 invertebrates, 12 vascular plants and a green alga. Although it has been predicted that evolution should inevitably lead to increasing mortality and declining fertility with age after maturity, there is great variation among these species, including increasing, constant, decreasing, humped and bowed trajectories for both long- and short-lived species. This diversity challenges theoreticians to develop broader perspectives on the evolution of ageing and empiricists to study the demography of more species.

Soil Microbiomes Underlie Population Persistence of an Endangered Plant Species.

Microbiomes can dramatically alter individual plant performance, yet how these effects influence higher-order processes is not well resolved. In particular, little is known about how microbiome effects on individual plants alter plant population dynamics, a question critical to imperiled species conservation. Here we integrate bioassays, multidecadal demographic data, and integral projection modeling to determine how the presence of the natural soil microbiome underlies plant population dynamics. Simulations indicated that the presence of soil microbiomes boosted population growth rates (λ) of the endangered Hypericum cumulicola by 13% on average, the difference between population growth versus decline in 76% of patches. The greatest benefit (47% increase in λ) occurred in low-nutrient, high-elevation habitats, suggesting that the soil microbiome may help expand H. cumulicola's distribution to include these stressful habitats. Our results demonstrate that soil microbiomes can significantly affect plant population growth and persistence and support the incorporation of soil microbiomes into conservation planning.

Dynamics of gaps, vegetation, and plant species with and without fire.

PREMISE OF THE STUDY: Areas lacking dominant plants, or gaps, can support high diversity and specialist species. Previous chronosequence research in Florida rosemary scrub showed indistinct gap area patterns with fire and the dependence of certain species on gaps. We hypothesized that fire and gap size would affect extinction, colonization, diversity, and vegetation composition. METHODS: In 2011-12, we revisited gaps first sampled in 2003, recording vascular plant and ground lichen occurrence by species, gap area, and burn history. We analyzed gap, vegetation, and species dynamics using linear mixed models, with Florida rosemary scrub patch as a random factor. KEY RESULTS: Gap areas declined quickly during the first 10 yr postfire and then stabilized. Between 2003 and 2011-12, unburned gaps usually remained extant or split, whereas burned gaps usually merged. Unburned gaps tended to shrink, whereas burned gaps became larger. Species richness was positively related to gap area, fire, and their interaction. Over time, richness declined in unburned gaps and increased in burned gaps. Local extinction and colonization of individual species were related to fire between 2003 and 2011-12. In burned gaps, ground lichens disappeared, but many herbaceous species, including those killed by fire, increased occupancy. Colonization of most species was favored by burning, large gaps, or both. CONCLUSIONS: In Florida rosemary scrub, fire and increasing gap size increased species richness and many individual species occurrences, reduced local extinctions, and increased colonizations. Therefore, land management activities that encourage the creation and maintenance of large gaps will promote biodiversity in this system.

Effects of habitat degradation, microsite, and seed density on the persistence of two native herbs in a subtropical shrubland.

PREMISE OF THE STUDY: Species in degraded ecosystems may interact differently with their surroundings from those under historic conditions. Understanding factors affecting variation in early life history stages of plants is fundamental to assessing their persistence in intact and degraded habitats, and the value of degraded lands. We evaluated the effect of seed density on the seed dynamics of two herbaceous species (annual, biennial), and considered how seed availability may influence population dynamics in different habitats (degraded, intact Florida scrub) and microsites (bare sand, leaf litter, shrub). METHODS: We used data on responses to experimental treatments (seed removal, seedling emergence, establishment) and models to evaluate how effects of these factors may change over time since the last disturbance. KEY RESULTS: Probability of any seed removal, emergence, and establishment per unit increased with seed density, although proportion removal for Chamaecrista fasciculata, proportion emergence for Balduina angustifolia, and proportion establishment for both species decreased with density. When animals were given selective access to seeds, invertebrates were primarily responsible for seed removal of both study species. Models with dynamics changing with time-since-disturbance for both species predicted that population growth may decrease slightly if local available seed density increases. CONCLUSIONS: Detailed demographic comparisons of populations in intact and degraded conditions can be used to understand the way that environmental conditions (habitat, microsite) combine with seed density effects to influence population dynamics of herb species. Degraded habitat may act as a transitional state in a trajectory toward intact conditions for some species, or as refugia for other native species.

Ability of matrix models to explain the past and predict the future of plant populations.

Uncertainty associated with ecological forecasts has long been recognized, but forecast accuracy is rarely quantified. We evaluated how well data on 82 populations of 20 species of plants spanning 3 continents explained and predicted plant population dynamics. We parameterized stage-based matrix models with demographic data from individually marked plants and determined how well these models forecast population sizes observed at least 5 years into the future. Simple demographic models forecasted population dynamics poorly; only 40% of observed population sizes fell within our forecasts' 95% confidence limits. However, these models explained population dynamics during the years in which data were collected; observed changes in population size during the data-collection period were strongly positively correlated with population growth rate. Thus, these models are at least a sound way to quantify population status. Poor forecasts were not associated with the number of individual plants or years of data. We tested whether vital rates were density dependent and found both positive and negative density dependence. However, density dependence was not associated with forecast error. Forecast error was significantly associated with environmental differences between the data collection and forecast periods. To forecast population fates, more detailed models, such as those that project how environments are likely to change and how these changes will affect population dynamics, may be needed. Such detailed models are not always feasible. Thus, it may be wiser to make risk-averse decisions than to expect precise forecasts from models.

Grassland intensification effects cascade to alter multifunctionality of wetlands within metaecosystems.

Sustainable agricultural intensification could improve ecosystem service multifunctionality, yet empirical evidence remains tenuous, especially regarding consequences for spatially coupled ecosystems connected by flows across ecosystem boundaries (i.e., metaecosystems). Here we aim to understand the effects of land-use intensification on multiple ecosystem services of spatially connected grasslands and wetlands, where management practices were applied to grasslands but not directly imposed to wetlands. We synthesize long-term datasets encompassing 53 physical, chemical, and biological indicators, comprising >11,000 field measurements. Our results reveal that intensification promotes high-quality forage and livestock production in both grasslands and wetlands, but at the expense of water quality regulation, methane mitigation, non-native species invasion resistance, and biodiversity. Land-use intensification weakens relationships among ecosystem services. The effects on grasslands cascade to alter multifunctionality of embedded natural wetlands within the metaecosystems to a similar extent. These results highlight the importance of considering spatial flows of resources and organisms when studying land-use intensification effects on metaecosystems as well as when designing grassland and wetland management practices to improve landscape multifunctionality.

Metacommunity dynamics over 16 years in a pyrogenic shrubland.

Metacommunity theory allows predictions about the dynamics of potentially interacting species' assemblages that are linked by dispersal, but strong empirical tests of the theory are rare. We analyzed the metacommunity dynamics of Florida rosemary scrub, a patchily distributed pyrogenic community, to test predictions about turnover rates, community nestedness, and responses to patch size, arrangement, and quality. We collected occurrence data for 45 plant species from 88 rosemary scrub patches in 1989 and 2005 and used growth form, mechanism of regeneration after fire, and degree of habitat specialization to categorize species by life history. We tested whether patch size, fire history, and structural connectivity (a measure of proximity and size of surrounding patches) could be used to predict apparent extinctions and colonizations. In addition, we tested the accuracy of incidence-function models built with the patch survey data from 1989. After fire local extinction rates were higher for herbs than woody plants, higher for species that regenerated only from seed than species able to resprout, and higher for generalist than specialist species. Fewer rosemary specialists and a higher proportion of habitat generalists were extirpated on recently burned patches than on patches not burned between 1989 and 2005. Nestedness was highest for specialists among all life-history groups. Estimated model parameters from 1989 predicted the observed (1989-2005) extinction rates and the number of patches with persistent populations of individual species. These results indicate that species with different life-history strategies within the same metacommunity can have substantially different responses to patch configuration and quality. Real metacommunities may not conform to certain assumptions of simple models, but incidence-function models that consider only patch size, configuration, and quality can have significant predictive accuracy.

Canopies, the Final Frog-tier: exploring responses of a specialist treefrog to prescribed fire in a pyrogenic ecosystem.

Background: Pine flatwoods of the southeastern United States were shaped by frequent fires. Land managers use prescribed fires to control fuels but also to restore historical fire dynamics. Broad outcomes of this practice are well-understood, but impacts on many organisms are still being explored. Frogs, for example, have upland and wetland requirements, limited mobility, and skin susceptible to desiccation. Treefrogs spend most of their lives in uplands away from water. When fire approaches, animals may escape to an unburned area, shelter in place, or be killed by the fire. We examined which of these mechanisms is the prevailing short-term response for a specialist treefrog in a pyrogenic flatwood system. Results: We assessed the short-term impacts of prescribed fire on the dynamics of an upland flatwood specialist, the pinewoods treefrog Dryophytes femoralis, using a replicated before-after-control-impact field experiment. We set pipes as treefrog refugia at 3 m, 6 m, 9 m, and 9+ m in 12 pine trees spread evenly across two treatments: reference trees in units burned in 2020 and trees in units with 2021 prescribed fire. Prescribed fires occurred on 16 April and 21 July 2021. Every 2 weeks between 5 March and 5 September, we checked pipes for frogs and assigned them unique color marks. We observed 78 individuals with 199 additional recaptures. We modeled abundance (as raw counts), survival, and vertical movement using mark-recapture methods, multi-state, and mixed linear models with a Bayesian framework. Survival and recapture were comparable among prescribed fire treatments, but abundances and movement probability varied. Frogs in trees in areas burned during the study were more likely to stay in place and less likely to descend to lower heights. We observed more frogs in trees after a 2021 fire compared to reference trees. Conclusions: The prevailing mechanism for resiliency to fire for pinewoods treefrogs was migration up large pines, then likely recolonization to lower vegetation layers when plants regreen post-fire. This substantiates conclusions from other works that the integrity of mature pines is key to sustaining native biodiversity. Future work and management should consider the three-dimensional structure of habitat when developing burn prescriptions and study designs.

Antecedentes: Las planicies de pinos del sudeste de los EEUU fueron modeladas por fuegos frecuentes. Allí, los manejadores de tierras usan las quemas prescriptas para controlar los combustibles vegetales, pero también para restaurar la dinámica de los incendios causados por rayos. Los resultados a gran escala están bien comprendidos, aunque los impactos sobre muchos organismos son todavía objeto de estudio. Las ranas, por ejemplo, tienen requerimientos particulares tanto en humedales como en tierras altas, dada su limitada movilidad y su piel sensible a la desecación. Las ranas que habitan en árboles (treefrogs) pasan la mayoría de sus vidas en tierras altas alejadas del agua. Cuando un incendio se aproxima, los animales pueden escapar hacia un área no quemada, guarecerse del fuego mediante una cobertura protectora, o ser muertas por el fuego. Examinamos cuál de esos mecanismos es la respuesta dinámica más prevalente en el corto plazo para la persistencia de una rana de árbol especialista en ese ecosistema pirogénico de planicies de pinos. Resultados: Determinamos los impactos a corto plazo de una quema prescripta en la dinámica de un especialista de esas planicies, la rana de los pinos Dryophytes femoralis, usando un experimento de campo replicado de antes-después- y control de impacto. Usamos tubos como refugios de ranas a 3, 6, 9, y más de 9 metros en 12 pinos distribuidos uniformemente entre dos tratamientos: árboles de referencia en unidades quemadas en 2020 y árboles en unidades quemadas en 2021 mediante quemas prescriptas. Las quemas prescriptas fueron realizadas en 16 de abril y 21 de julio de 2021. Cada dos semanas entre el 5 de marzo y el 5 de setiembre, revisamos los tubos con ranas y le asignamos marcas de color únicas. Observamos 78 individuos con 199 recapturas adicionales. Modelamos la abundancia (como conteos crudos), supervivencia y movimientos verticales usando el método de marcas de recaptura, estados múltiples y modelos lineales mixtos dentro de un marco Bayesiano. La supervivencia y recaptura fueron comparables entre los tratamientos de quemas prescriptas, aunque la abundancia y la probabilidad del movimiento variaron. Las ranas en los árboles en las áreas quemadas durante el estudio fue más probable que se quedaran en su lugar a que descendieran a lugares más bajos. Observamos más ranas en árboles luego de la quema del 2021 comparadas con las que estaban en árboles de referencia. Conclusiones: El mecanismo prevalente para la resiliencia al fuego para las ranas de árboles fue la migración hacia pinos más grandes, y luego recolonizar lugares más bajos cuando las planteas reverdecen en el post-fuego. Estas conclusiones se consustancian con otros trabajos en que la integridad de los pinos maduros es clave para sostener la biodiversidad nativa. Trabajos de investigación futuros y prácticas de manejo deberían considerar la estructura tridimensional del hábitat cuando se desarrollen prescripciones de quema y diseños de estudio.

Incorporating distance metrics and temporal trends to refine mixed stock analysis.

The distribution of marine organisms is shaped by geographic distance and oceanographic features like currents. Among migratory species, individuals from multiple populations may share feeding habitats seasonally or across life stages. Here, we introduce a modification for many-to-many mixed stock models to include distance between breeding and foraging sites as an ecological covariate and evaluate how the composition of green turtle, Chelonia mydas, juvenile mixed stock aggregations changed in response to population growth over time. Our modified many-to-many model is more informative and generally tightens credible intervals over models that do not incorporate distance. Moreover, we identified a decrease in genetic diversity in a Florida nesting site and two juvenile aggregations. Mixed stock aggregations in central Florida have changed from multiple sources to fewer dominant source populations over the past ~ 20 years. We demonstrate that shifts in contributions from source populations to mixed stock aggregations are likely associated with nesting population growth. Furthermore, our results highlight the importance of long-term monitoring and the need for periodical reassessment of reproductive populations and juvenile aggregations. Understanding how mixed stock aggregations change over time and how different life stages are connected is fundamental for the development of successful conservation plans for imperiled species.

How do plant ecologists use matrix population models?

Matrix projection models are among the most widely used tools in plant ecology. However, the way in which plant ecologists use and interpret these models differs from the way in which they are presented in the broader academic literature. In contrast to calls from earlier reviews, most studies of plant populations are based on < 5 matrices and present simple metrics such as deterministic population growth rates. However, plant ecologists also cautioned against literal interpretation of model predictions. Although academic studies have emphasized testing quantitative model predictions, such forecasts are not the way in which plant ecologists find matrix models to be most useful. Improving forecasting ability would necessitate increased model complexity and longer studies. Therefore, in addition to longer term studies with better links to environmental drivers, priorities for research include critically evaluating relative/comparative uses of matrix models and asking how we can use many short-term studies to understand long-term population dynamics.

Fine-scale spatial variation in fitness is comparable to disturbance-induced fluctuations in a fire-adapted species.

The spatial scale at which demographic performance (e.g., net reproductive output) varies can profoundly influence landscape-level population growth and persistence, and many demographically pertinent processes such as species interactions and resource acquisition vary at fine scales. We compared the magnitude of demographic variation associated with fine-scale heterogeneity (<10 m), with variation due to larger-scale (>1 ha) fluctuations associated with fire disturbance. We used a spatially explicit model within an IPM modeling framework to evaluate the demographic importance of fine-scale variation. We used a measure of expected lifetime fruit production, EF , that is assumed to be proportional to lifetime fitness. Demographic differences and their effects on EF were assessed in a population of the herbaceous perennial Hypericum cumulicola (~2,600 individuals), within a patch of Florida rosemary scrub (400 × 80 m). We compared demographic variation over fine spatial scales to demographic variation between years across 6 yr after a fire. Values of EF changed by orders of magnitude over <10 m. This variation in fitness over fine spatial scales (<10 m) is commensurate to postfire changes in fitness for this fire-adapted perennial. A life table response experiment indicated that fine-scale spatial variation in vital rates, especially survival, explains as much change in EF as demographic changes caused by time-since-fire, a key driver in this system. Our findings show that environmental changes over a few tens of meters can have ecologically meaningful implications for population growth and extinction.

Demographic effects of interacting species: exploring stable coexistence under increased climatic variability in a semiarid shrub community.

Population persistence is strongly determined by climatic variability. Changes in the patterns of climatic events linked to global warming may alter population dynamics, but their effects may be strongly modulated by biotic interactions. Plant populations interact with each other in such a way that responses to climate of a single population may impact the dynamics of the whole community. In this study, we assess how climate variability affects persistence and coexistence of two dominant plant species in a semiarid shrub community on gypsum soils. We use 9 years of demographic data to parameterize demographic models and to simulate population dynamics under different climatic and ecological scenarios. We observe that populations of both coexisting species may respond to common climatic fluctuations both similarly and in idiosyncratic ways, depending on the yearly combination of climatic factors. Biotic interactions (both within and among species) modulate some of their vital rates, but their effects on population dynamics highly depend on climatic fluctuations. Our results indicate that increased levels of climatic variability may alter interspecific relationships. These alterations might potentially affect species coexistence, disrupting competitive hierarchies and ultimately leading to abrupt changes in community composition.

A solution to minimum sample size for regressions.

Regressions and meta-regressions are widely used to estimate patterns and effect sizes in various disciplines. However, many biological and medical analyses use relatively low sample size (N), contributing to concerns on reproducibility. What is the minimum N to identify the most plausible data pattern using regressions? Statistical power analysis is often used to answer that question, but it has its own problems and logically should follow model selection to first identify the most plausible model. Here we make null, simple linear and quadratic data with different variances and effect sizes. We then sample and use information theoretic model selection to evaluate minimum N for regression models. We also evaluate the use of coefficient of determination (R2) for this purpose; it is widely used but not recommended. With very low variance, both false positives and false negatives occurred at N < 8, but data shape was always clearly identified at N ≥ 8. With high variance, accurate inference was stable at N ≥ 25. Those outcomes were consistent at different effect sizes. Akaike Information Criterion weights (AICc wi) were essential to clearly identify patterns (e.g., simple linear vs. null); R2 or adjusted R2 values were not useful. We conclude that a minimum N = 8 is informative given very little variance, but minimum N ≥ 25 is required for more variance. Alternative models are better compared using information theory indices such as AIC but not R2 or adjusted R2. Insufficient N and R2-based model selection apparently contribute to confusion and low reproducibility in various disciplines. To avoid those problems, we recommend that research based on regressions or meta-regressions use N ≥ 25.

Comment on "The extent of forest in dryland biomes".

The study by Bastin et al (Reports, 12 May 2017, p. 635) is based on an incomplete delimitation of dry forest distribution and on an old and incorrect definition of drylands. Its sampling design includes many plots located in humid ecosystems and ignores critical areas for the conservation of dry forests. Therefore, its results and conclusions may be unreliable.

Fire-mediated effects of shrubs, lichens and herbs on the demography of Hypericum cumulicola in patchy Florida scrub.

Understanding the effect of disturbance and interspecific interactions on population dynamics and availability of suitable habitats for colonization and growth is critical for conservation and management of endangered species. Hypericum cumulicola is a narrowly endemic, small perennial herb virtually restricted to open areas of well-drained white sand in Florida rosemary scrub, a naturally patchy community that burns about every 20-80 years. Over 1 year (September 1994 to September 1995) we evaluated variation in survival, growth and fecundity among 1214 individuals in 14 rosemary scrub patches of different sizes (0.09-1.85 ha) and fire histories (2, 8-10, and >20 years since the last fire). Fire kills aboveground individuals of H. cumulicola, but new individuals were present a year after fire. Recruitment decreased in patches more than a decade post-fire. Survival, annual height growth rate, and fecundity (number of flowers and fruits) were higher in recently burned patches. Scrub patch size did not affect these demographic variables. Survival was positively associated with the presence of conspecifics and negatively related to proximity to the dominant shrub Florida rosemary (Ceratiola ericoides), prior reproductive output, and ground lichen cover. Since H. cumulicola and other herbaceous species in the rosemary scrub depend on sporadic fires to decrease interference of shrubs and ground lichens, its persistence may be threatened by fire suppression.

Genetic change following fire in populations of a seed-banking perennial plant.

Disturbances such as fire have the potential to remove genetic variation, but seed banks may counter this loss by restoring alleles through a reservoir effect. We used allozyme analysis to characterize genetic change in two populations of the perennial Hypericum cumulicola, an endemic of the fire-prone Florida scrub. We assessed genetic variation before and 1, 2, and 3 years after fire that killed nearly all aboveground plants. Populations increased in size following fire, with most seedlings likely recruited from a persistent seed bank. Four of five loci were variable. Most alleles were present in low frequencies, but our large sample sizes allowed detection of significant trends. Expected heterozygosity increased, and allele presence and allele frequencies showed marked shifts following fire. The post-fire seedling cohort contained new alleles to the study and one new allele to the species. Population differentiation between the two study sites did not change. Our study is the first to directly documents genetic changes following fire, a dominant ecological disturbance worldwide, and is also one of the few to consider shifts in a naturally recruiting post-disturbance seedling cohort. We demonstrate the potential of seed banks to restore genetic variation lost between disturbances. Our study demonstrates that rapid genetic change can occur with disturbance and that fire can have positive effects on the genetics of rare species.

Genetic insights into the biogeography of the southeastern North American endemic, Ceratiola ericoides (Empetraceae).

The southeastern United States harbors an unusually large number of endemic plant taxa, which may reflect the refugial nature of the region during Pleistocene glacial maxima. Understanding the genetic diversity and structure of extant plant taxa can provide insights into the biogeographical processes that shaped them genetically. Here, we investigate the levels and partitioning of allozyme diversity in the southeastern North American endemic, Ceratiola ericoides, which displayed greater genetic variation and structure than other endemics. Central Florida populations represent a center of genetic diversity, whereas South Carolina and Georgia Fall Line sandhill populations have a subset of the Central Florida genetic diversity and may be relicts of a once continuous distribution. This much broader, continuous distribution throughout the southeastern United States occurred during glacial maxima when the scrub habitat, dominated by C. ericoides, expanded considerably owing to drier climatic conditions. Georgia Coastal Plain populations appear to have been independently founded more recently by propagules from Central Florida and the Fall Line sandhills because they have an even more limited subset of genetic diversity and greater genetic heterogeneity among populations. Since their establishment, coastal plain populations appear to have had little, if any, gene exchange among each other or with the relatively proximate Fall Line sandhill populations. These data underscore the importance of understanding the genetic composition and historical biogeography of species before intelligent management or restoration decisions can be made regarding their preservation.

Using population viability analysis to predict the effects of climate change on the extinction risk of an endangered limestone endemic shrub, Arizona cliffrose.

The threat of global warming to rare species is a growing concern, yet few studies have predicted its effects on rare populations. Using demographic data gathered in both drought and nondrought years between 1996-2003 in central Arizona upper Sonoran Desert, we modeled population viability for the federally endangered Purshia subintegra (Kearney) Henrickson (Arizona cliffrose). We used deterministic matrix projection models and stochastic models simulating weather conditions during our study, given historical weather variation and under scenarios of increased aridity. Our models suggest that the P. subintegra population in Verde Valley is slowly declining and will be at greater risk of extinction with increased aridity. Across patches at a fine spatial scale, demographic performance was associated with environmental factors. Moist sites (patches with the highest soil moisture, lowest sand content, and most northern aspects) had the highest densities, highest seedling recruitment, and highest risk of extinction over the shortest time span. Extinction risk in moist sites was exacerbated by higher variance in recruitment and mortality. Dry sites had higher cumulative adult survival and lower extinction risk but negative growth rates. Steps necessary for the conservation of the species include introductions at more northern latitudes and in situ manipulations to enhance seedling recruitment and plant survival. We demonstrate that fine spatial-scale modeling is necessary to predict where patches with highest extinction risk or potential refugia for rare species may occur Because current climate projections for the 21st century imply range shifts at rates of 300 to 500 km/century, which are beyond even exceptional examples of shifts in the fossil record of 100-150 km, it is likely that preservation of many rare species will require human intervention and a long-term commitment. Global warming conditions are likely to reduce the carrying capacity of many rare species' habitats.