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

Exploring population responses to environmental change when there is never enough data: a factor analytic approach

© 2018 The Authors. Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of British Ecological Society Temporal variability in the environment drives variation in vital rates, with consequences for population dynamics and life-history evolution. Integral projection models (IPMs) are data-driven structured population models widely used to study population dynamics and life-history evolution in temporally variable environments. However, many datasets have insufficient temporal replication for the environmental drivers of vital rates to be identified with confidence, limiting their use for evaluating population level responses to environmental change. Parameter selection, where the kernel is constructed at each time step by randomly selecting the time-varying parameters from their joint probability distribution, is one approach to including stochasticity in IPMs. We consider a factor analytic (FA) approach for modelling the covariance matrix of time-varying parameters, whereby latent variable(s) describe the covariance among vital rate parameters. This decreases the number of parameters to estimate and, where the covariance is positive, the latent variable can be interpreted as a measure of environmental quality. We demonstrate this using simulation studies and two case studies. The simulation studies suggest the FA approach provides similarly accurate estimates of stochastic population growth rate to estimating an unstructured covariance matrix. We demonstrate how the latent parameter can be perturbed to show how selection on reproductive delays in the monocarp Carduus nutans changes under different environmental conditions. We develop a demographic model of the fire dependent herb Eryngium cuneifolium to show how a putative driver of the variation in environmental quality can be incorporated with the addition of a single parameter. Using perturbation analyses we determine optimal management strategies for this species. This approach estimates fewer parameters than previous approaches and allows novel eco-evolutionary insights. Predictions on population dynamics and life-history evolution under different environmental conditions can be made without necessarily identifying causal factors. Putative environmental drivers can be incorporated with relatively few parameters, allowing for predictions on how populations will respond to changes in the environment

The implications of seasonal climatic effects for managing disturbance dependent populations under a changing climate

The frequency of ecological disturbances, such as fires, is changing due to changing land use and climatic conditions. Disturbance-adapted species may thus require the manipulation of disturbance regimes to persist. However, the effects of changes in other abiotic factors, such as climatic conditions, are frequently disregarded in studies of such systems. Where climatic effects are included, relatively simple approaches that disregard seasonal variation in the effects are typically used. We compare predictions of population persistence using different fire return intervals (FRIs) under recent and predicted future climatic conditions for the rare fire-dependent herb Eryngium cuneifolium. We used functional linear models (FLMs) to estimate the cumulative effect of climatic variables across the annual cycle, allowing the strength and direction of the climatic impacts to differ over the year. We then estimated extinction probabilities and minimum population sizes under past and forecasted future climatic conditions and a range of FRIs. Under forecasted climate change, E. cuneifolium is predicted to persist under a much broader range of FRIs, because increasing temperatures are associated with faster individual growth. Climatic impacts on fecundity do not result in a temporal trend in this vital rate due to antagonistic seasonal effects operating through winter and summer temperatures. These antagonistic seasonal climatic effects highlight the importance of capturing the seasonal dependence of climatic effects when forecasting their future fate. Synthesis. Awareness of the potential effects of climate change on disturbance-adapted species is necessary for developing suitable management strategies for future environmental conditions. However, our results suggest that widely used simple methods for modelling climate impacts, that disregard seasonality in such effects, may produce misleading inferences

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 (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

Seed Bank Changes with Time-Since-Fire In Florida Rosemary Scrub

The soil seed bank plays a central role in the regeneration of obligate seeding species in fire-prone habitats. We evaluated how seed density and species composition changed with time-since-fire in the Florida, USA, rosemary scrub community. Because fire affects habitat availability and plant demographic variation, we predicted that soil seed density would be low in recently burned and long-unburned stands and high at intermediate time-since-fire. Seed bank soil samples were collected from a chronosequence of time-since-fire composited from two trials conducted in 1992-1993 and 2008-2009: two sites each of 3, 6, 10, and 24 years post-fire, and 3 long-unburned (similar to 67 years) sites. The seedling emergence method was used to determine species composition of the seed bank. Across all time-since-fire age classes, herbaceous species dominated the seed bank, while long-lived subshrubs and shrubs were present in low densities. Seed banks from sites three years post-fire were distinct from the other sites. When species were sorted as functional groups, seed density was related with time-since-fire for subshrubs and ruderal herbs, but not for scrub herbs and graminoids. Subshrubs and ruderal herbs had highest seed densities in recently burned stands. Seed densities of Florida rosemary (Ceratiola ericoides Michx.) (the major obligate seeding shrub in this community) were associated with time-since-fire and showed highest densities at recently burned and long-unburned sites. The seed banks of two scrub herb species, paper nailwort (Paronychia chartacea Fernald) and nodding pinweed (Lechea cernua Small), were associated with time-since-fire. They reached peaks in density in the first ten years post-fire, corresponding with similar changes in their aboveground abundances with time-since-fire. Soil seed densities of several species and functional groups were associated with time-since-fire, but timing of peak seed density varied depending on species\u27 life span and age of reproductive maturity

Population Viability With Fire In Eryngium Cuneifolium: Deciphering A Decade Of Demographic Data

We analyzed and modeled the demography of Eryngium cuneifolium, an herbaceous species endemic to the fire-prone Florida scrub, using 10 annual censuses (1990-1999) of 11 populations at Archbold Biological Station. Nearly every aspect of the demography of this plant is affected by time since fire. Year, time since fire, life history stage, and plant age affected survival, growth, and fecundity of E. cuneifolium, but time since fire and life history stage had the most consistent effects. Survival, flowering stem production, and early seedling survival were highest in recently burned sites. Long-term survival, growth, and fecundity were highest for yearling cohorts recruiting recently after fire, with the largest contrast between plants recruiting two years postfire and those recruiting more than a decade postfire. Prior (historical) stage also affected individual plant fates. For example, plants with prior stasis or regression in stage subsequently died in greater numbers than plants with prior advancement in stage. Historical analyses did not suggest any cost associated with the initiation of flowering. We used a matrix selection approach to explicitly model Eryngium cuneifolium population viability in relation to fire. This simulation strategy included preserving observed data and variances within projection matrices formed for individual combinations of population and year. We built 54 of these matrices, each with six stages (seed bank, yearlings, vegetative plants, and three reproductive stages). Each of these matrices also represented a specific time since fire. In building matrices, we minimized the use of pooled data while retaining specific matrices whenever possible. In this way, we preserved both the correlation structure within individual matrices (populations, years) and protected patterns among matrices across the time-since-fire gradient. To deal with less-detailed data on recruitment processes, we evaluated 13 fertility and seed bank scenarios that bracketed a range of outcomes. All scenarios were similar in showing the positive effects of fire on the demography of E. cuneifolium. The scenario with high seed bank survival (0.5) and low germination rates (0-0.005) was the best predictor of observed postfire years of peak aboveground population size (∼8 yr) and aboveground population disappearance (30-34 yr), and also did a good job of reproducing observed population trajectories. Finite rates of increase (λ) were \u3e 1 only during the first decade postfire but then declined beyond a decade postfire. Although prior (historical) stage affected most individual demographic parameters, it did not significantly influence finite rates of increase. Elasticities were highest for stasis and germination from the seed bank. Elasticities for survival increased with time since fire, while growth and fertility elasticities decreased. In historical models (those with information on stage from the second-to-last year), the elasticities for stasis were higher and the elasticities for growth lower, compared to models without this history. Bootstrapping suggested small standard errors for several types of model output. Most matrix elements were positively correlated, suggesting that favorable conditions affect many life history stages similarly, and that simulations using element selection would provide a less conservative risk assessment than the matrix selection technique used. We used a stochastic simulation program to simulate changing demography with time since fire, with various fire-return intervals, and for various initial population sizes. We obtained estimates of extinction risk and probability of population decline. Even populations as large as thousands of individuals will become extinct in the absence of fire. Fire-return intervals of 15 yr or less are necessary for E. cuneifolium persistence at individual sites. Fires at intervals longer than 20 yr create substantial extinction risks, and intervals longer than 12 yr produce declining populations. Cycles of widely divergent, alternating short and long fire-return intervals caused slightly higher chances of extinction compared to regular fire-return intervals. Although shrub regrowth is implicated in the decreased viability of E. cuneifolium populations under regimes of infrequent fire, aboveground fuel increases are often too slow to allow frequent burning in Florida rosemary scrub. If E. cuneifolium\u27s rosemary scrub habitat burns less often than every 20 yr, local extinctions and metapopulation dynamics may be the norm. Other rosemary scrub specialists (e.g., Hypericum cumulicola) thrive with less frequent fires and persist in smaller gaps among the regrowing shrubs. Therefore, we suggest that temporal variation in fire-return intervals and spatial variation in fire intensity and patchiness (pyrodiversity) will allow coexistence of all Florida scrub species and hedge against local extinctions of specialists like E. cuneifolium. © 2004 by the Ecological Society of America

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

Afinidad fitogeográfica y papel sucesional de la flora leñosa de los bosques de pino‑encino de los Altos de Chiapas, México

A successional role for each phytogeographical group of seral stands of the pine-oak forests in the Highlands of Chiapas (southern Mexico) could be established after their structural analysis. Most of the Holarctic elements regenerate in early successional conditions, while the regeneration of many Andean and East Asian elements is restricted to the more advanced stands. Forest structure and floristic composition appears as the result of a mixture of species belonging to genera of diverse origin. Their local coexistence seems to depend on their tolerance to those environmental conditions resulting from forest development through succession. We ascribe a central role to the canopy species belonging to Holarctic genera which determine the understory microhabitat for most of the remaining woody species, notably for those of Andean affinity.El análisis de la estructura de varias etapas serales de los bosques húmedos de pino-encino de Los Altos de Chiapas permitió establecer un papel sucesional particular para los distintos grupos de afinidad florística que los componen. La mayoría de los elementos holárticos muestran amplia regeneración en etapas sucesionalmente tempranas, mientras que la de muchos de los elementos andinos y de afinidad con el este de Asia sólo ocurre en condiciones más avanzadas. La estructura y la composición de estos bosques parecen resultar de una mezcla de especies pertenecientes a géneros de origen diverso, cuya coexistencia local depende de su propia tolerancia a las condiciones ambientales que se crean durante la sucesión forestal. Las especies del dosel superior, que pertenecen a géneros de afinidad holártica, juegan un papel central al determinar las condiciones ambientales del interior del bosque, a las cuales se encuentran supeditadas la mayoría de los demás componentes leñosos, especialmente los del grupo de afinidad andina

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 withtheir 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). M ETHODS: 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 withseed density, although proportion removal for Chamaecrista fasciculata, proportion emergence for Balduina angustifolia, and proportion establishment for bothspecies decreased withdensity. When animals were given selective access to seeds, invertebrates were primarily responsible for seed removal of bothstudy species. Models withdynamics changing withtime-since-disturbance for bothspecies predicted that population growthmay 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 withseed 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