Biology subjects

Salguero-Gomez, R.

Publications and source records attributed to Salguero-Gomez, R..

At least 73 records · Page 4Linked to original sources

bioRxiv2022

Flexible estimation of biodiversity with short-range multispectral imaging in a temperate grassland

O_LIImage sensing technologies are rapidly increasing the cost-effectiveness of biodiversity monitoring efforts. Species differences in the reflectance of electromagnetic radiation have recently been highlighted as a promising target to estimate plant biodiversity using multispectral image data. C_LIO_LIHowever, these efforts are currently hampered by logistical difficulties in broad-scale implementation and their use in characterizing biodiversity at different spatial scales. C_LIO_LIHere, we investigate the utility of multispectral imaging technology from commercially available unmanned aerial vehicles (UAVs, or drones) in estimating biodiversity metrics at short-range (<10 m image recording height) in a temperate calcareous grassland ecosystem in Oxfordshire, UK. We calculate a suite of moments (coefficient of variation, standard deviation, skew, kurtosis) for the distribution of radiance from multispectral images at five wavelength bands (Blue 450{+/-}16 nm; Green 560{+/-}16 nm; Red 650{+/-}16 nm; Red Edge 730{+/-}16 nm; Near Infrared 840{+/-}16 nm) and test their effectiveness at estimating ground-truthed biodiversity metrics from in-situ botanical surveys for 37 - 1 m x 1 m quadrats. C_LIO_LIWe find positive associations between the average coefficient of variation in spectral radiance and both the Shannon-Weiner and Simpsons biodiversity indices. Furthermore, we find that the average coefficient of variation in spectral radiance is consistent and highly repeatable, across sampling days and recording heights. Positive associations with biodiversity indices hold irrespective of the image recording height (2-8 m), but we report reductions in estimates of spectral diversity with increases to UAV recording height. UAV imaging reduced sampling time by 16-fold relative to in-situ botanical surveys. C_LIO_LISynthesis - We demonstrate the utility of multispectral radiance moments as an indicator of grassland biodiversity metrics at high spatial resolution using a widely available UAV monitoring system at a coarse spectral resolution. The use of UAV technology with multispectral sensors has far-reaching potential to provide cost-effective and high-resolution monitoring of biodiversity in complex environments. C_LI

ecology↗

bioRxiv2022

Rpadrino: an R package to access and use PADRINO, an open access database of Integral Projection Models

O_LIDiscrete time structured population projection models are an important tool for studying population dynamics. Within this field, Integral Projection Models (IPMs) have become a popular method for studying populations structured by continuously distributed traits (e.g. height, weight). Databases of discrete time, discrete state structured population models, for example DATLife (life tables) and COMPADRE & COMADRE (matrix population models), have made quantitative syntheses straightforward to implement. These efforts allow researchers to address questions in both basic and applied ecology and evolutionary biology. There are now over 300 peer-reviewed publications containing IPMs. We describe a novel framework to quickly reconstruct these models for subsequent analyses using Rpadrino R package, which serves as an interface to PADRINO, a new database of structured population models. C_LIO_LIWe introduce an R package, Rpadrino, which enables users to download, subset, reconstruct, and extend published IPMs. Rpadrino makes use of recently created software, ipmr, to provide an engine to reconstruct a wide array of IPMs from their symbolic representations and conduct subsequent analyses. Rpadrino and ipmr are extensively documented to help users learn their usage. C_LIO_LIRpadrino currently enables users to reconstruct 280 IPMs from 40 publications that describe the demography of 14 animal and 26 plant species. All of these IPMs are tested to ensure they reproduce published estimates. Rpadrino provides an interface to augment PADRINO with external data and modify parameter values, creating a platform to extend models beyond their original purpose while retaining full reproducibility. C_LIO_LIPADRINO and Rpadrino provide a toolbox for asking new questions and conducting syntheses with peer-reviewed published IPMs. Rpadrino provides a user-friendly interface so researchers do not need to worry about the database structure or syntax, and can focus on their research questions and analyses. Additionally, Rpadrino is thoroughly documented, and provides numerous examples of how to perform analyses which are not included in the packages functionality. C_LI

ecology↗

bioRxiv2021

Life history adaptations to fluctuating environments: Combined effects of demographic buffering and lability of vital rates

Demographic buffering and lability have been identified as adaptive strategies to optimise fitness in a fluctuating environment. These are not mutually exclusive, however we lack efficient methods to measure their relative importance for a given life history. Here, we decompose the stochastic growth rate (fitness) into components arising from nonlinear responses and variance-covariance of demographic parameters to an environmental driver, which allows studying joint effects of buffering and lability. We apply this decomposition for 154 animal matrix population models under different scenarios, to explore how these main fitness components vary across life histories. Faster-living species appear more responsive to environmental fluctuations, either positively or negatively. They have the highest potential for strong adaptive demographic lability, while demographic buffering is a main strategy in slow-living species. Our decomposition provides a comprehensive framework to study how organisms adapt to variability through buffering and lability, and to predict species responses to climate change.

ecology↗

bioRxiv2021

Coral assemblages at higher latitudes favour short-term potential over long-term performance

The persistent exposure of coral communities to more variable abiotic regimes is assumed to augment their resilience to future climatic variability. Yet, while the determinants of coral population resilience across species remain unknown, we are unable to predict the winners and losers across reef ecosystems exposed to increasingly variable conditions. Using annual surveys of 3171 coral individuals across Australia and Japan (2017-2019), we explore spatial variation across the short- and long-term dynamics of competitive, stress-tolerant, and weedy assemblages to evaluate how thermal variability mediates the structural composition of coral communities. We illustrate how, by promoting short-term potential over long-term performance, coral assemblages can reduce their vulnerability to stochastic environments. However, compared to stress-tolerant, and weedy assemblages, competitive coral taxa display a reduced capacity for elevating their short-term potential. Accordingly, future climatic shifts threaten the structural complexity of coral assemblages in variable environments, emulating the degradation expected across global tropical reefs.

ecology↗

bioRxiv2021

Human pressures filter out the less resilient demographic strategies in natural populations of plants and animals worldwide

Human activities are drastically reshaping Earths ecosystems. Across the tree of life, species become threatened and ultimately go extinct when they are unable to cope with these changes. Hence, understanding the resilience of natural populations is necessary to understand and predict species capacity to cope with increasing human pressures. Here, we use high-resolution demographic information for 921 populations of wild plants and animals to assess how they respond to increasing levels of human pressure. We show that fewer successful resilience strategies, allowing population to persist in disturb environments, exist in human-influenced habitats compared to pristine habitats. In contrast, pristine habitats host species with higher resistance and faster recovery than more altered environments. Importantly, the examined macroecologial patterns of demographic resilience are kingdom- and mobility-specific: natural populations of plants recover faster and have a propensity to grow faster after a disturbance (i.e., compensation) in urban areas than in pristine habitats, while these tendencies do not appear in animals. Likewise, populations of animals with limited mobility are less able to resist or compensate for disturbances in human altered environments than highly mobile populations. Our results suggest that human activities have eroded the diversity of natural populations resilience strategies. This finding implies that species will be less tolerant to disturbance in the future, as continuing biodiversity loss and increasing human impacts will ultimately shrink the spectrum of resilience strategies of organisms.

ecology↗

bioRxiv2021

Life history mediates the trade-offs among different components of demographic resilience

Summary paragraphAccelerating rates of biodiversity loss underscore the need to understand how species achieve resilience -their ability to resist and recover from a/biotic disturbances. Yet, the factors determining the resilience of species remain poorly understood, due to disagreements on its definition and the lack of large-scale analyses. Here, we investigate how the life history of 785 natural populations of animals and plants predict their intrinsic ability to be resilient. We show that demographic resilience can be achieved through different combinations of compensation, resistance, and recovery after a disturbance. We demonstrate that these resilience components are highly correlated with life history traits related to the species pace of life and reproductive strategy. Species with longer generation times require longer recovery times post-disturbance, while those with greater reproductive capacity have greater resistance and compensation. Our findings highlight the key role of life history traits to understand species resilience, improving our ability to predict how natural populations cope with disturbance regimes.

ecology↗

bioRxiv2021

Beyond demographic buffering: Context dependence in demographic strategies across animals

Temporal variation in vital rates (e.g., survival, reproduction) can decrease the long-term mean performance of a population. Species are therefore expected to evolve demographic strategies that counteract the negative effects of vital rate variation on the population growth rate. One key strategy, demographic buffering, is reflected in a low temporal variation in vital rates critical to population dynamics. However, comparative studies in plants have found little evidence for demographic buffering, and little is known about the prevalence of buffering in animal populations. Here, we used vital rate estimates from 31 natural populations of 29 animal species to assess the prevalence of demographic buffering. We modeled the degree of demographic buffering using a standard measure of correlation between the standard deviation of vital rates and the sensitivity of the population growth rate to changes in such vital rates across populations. We also accounted for the effects of life-history traits, i.e., age at first reproduction and spread of reproduction across the life cycle, on these correlation measures. We found no strong or consistent evidence of demographic buffering across the study populations. Instead, key vital rates could vary substantially depending on the specific environmental context populations experience. We suggest that it is time to look beyond concepts of demographic buffering when studying natural populations towards a stronger focus on the environmental context-dependence of vital-rate variation.

ecology↗

bioRxiv2021

Transient amplification enhances the persistence of tropicalising coral populations in marginal high latitude environments.

Predicting the viability of species exposed to increasing climatic stress requires an appreciation for the mechanisms underpinning the success or failure of marginal populations. Rather than traditional metrics of long-term population performance, here we illustrate that short-term (i.e. transient) demographic characteristics, including measures of resistance, recovery, and compensation, are fundamental in the poleward range expansion of hard corals, facilitating the establishment of coral populations at higher-latitudes. Through the annual census of tropical and subtropical Acropora spp. colonies in Japan, between 2017-2019, we show how the transient amplification potential of a subtropical coral population supports its enhanced growth within unstable environmental conditions. The transient dynamics of both the tropical and subtropical populations were strongly influenced by their corresponding recruitment patterns. However, we demonstrate that variation in colony survival and fragmentation patterns between the two populations determines their relative capacities for transient amplification. This latitudinal variation in the transient dynamics of Acropora spp. populations emphasizes that coral populations can possess the demographic plasticity necessary for exploiting more variable, marginal conditions.

ecology↗

bioRxiv2021

Plant demographic knowledge is biased towards short-term studies of temperate-region herbaceous perennials

O_LIPlant population dynamics research has a long history, and data collection rates have increased through time. The inclusion of this information in databases enables researchers to investigate the drivers of demographic patterns globally and study life history evolution. C_LIO_LIStudies aiming to generalise demographic patterns rely on data being derived from a representative sample of populations. However, the data are likely to be biased, both in terms of the species and ecoregions investigated and in how the original studies were conducted. C_LIO_LIMatrix population models (MPMs) are a widely-used tool in plant demography, so an assessment of publications that have used MPMs is a convenient way to assess the distribution of plant demographic knowledge. We assessed bias in this knowledge using data from the COMPADRE Plant Matrix Database, which contains MPMs for almost 800 plant species. C_LIO_LIWe show that tree species and tropical ecoregions are under-represented, while herbaceous perennials and temperate ecoregions are over-represented. In addition, there is a positive association between the number of studies per country and the wealth of the country. Furthermore, we found a strong tendency towards low spatiotemporal replication: More than 50% of the studies were conducted over fewer than 4 years, and only 17% of the studies have replication across >3 sites. This limited spatiotemporal coverage means that the data may not be representative of the environmental conditions experienced by the species. C_LIO_LISynthesis: The biases and knowledge gaps we identify are a challenge for the progress of theory and limit the usefulness of current data for determining patterns that would be useful for conservation decisions, such as determining general responses to climate change. We urge researchers to close these knowledge gaps with novel data collection. C_LI

ecology↗

bioRxiv2021

Rcompadre and Rage - two R packages to facilitate the use of the COMPADRE and COMADRE databases and calculation of life history traits from matrix population models

O_LIMatrix population models (MPMs) are an important tool for biologists seeking to understand the causes and consequences of variation in vital rates (e.g., survival, reproduction) across life cycles. Empirical MPMs describe the age- or stage-structured demography of organisms and usually represent the life history of a population during a particular time frame at a specific geographic location. C_LIO_LIThe COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database are the most extensive resources for MPM data, collectively containing >12,000 individual projection matrices for >1,100 species globally. Although these databases represent an unparalleled resource for researchers, land managers, and educators, the current computational tools available to answer questions with MPMs impose significant barriers to potential COM(P)ADRE database users by requiring advanced knowledge to handle diverse data structures and program custom analysis functions. C_LIO_LITo close this knowledge gap, we present two interrelated R packages designed to (i) facilitate the use of these databases by providing functions to acquire, quality control, and manage both the MPM data contained in COMPADRE and COMADRE, and a users own MPM data (Rcompadre), and (ii) present a range of functions to calculate life history traits from MPMs in support of ecological and evolutionary analyses (Rage). We provide examples to illustrate the use of both. C_LIO_LIRcompadre and Rage will facilitate demographic analyses using MPM data and contribute to the improved replicability of studies using these data. We hope that this new functionality will allow researchers, land managers, and educators to unlock the potential behind the thousands of MPMs and ancillary metadata stored in the COMPADRE and COMADRE matrix databases, and in their own MPM data. C_LI

ecology↗

bioRxiv2021

ipmr: Flexibly implement Integral Projection Models in R

O_LIIntegral projection models (IPMs) are an important tool for studying the dynamics of populations structured by one or more continuous traits (e.g. size, height, color). Researchers use IPMs to investigate questions ranging from linking drivers to plant population dynamics, planning conservation and management strategies, and quantifying selective pressures in natural populations. The popularity of stage-structured population models has been supported by R scripts and packages (e.g. IPMpack, popbio, popdemo, lefko3) aimed at ecologists, which have introduced a broad repertoire of functionality and outputs. However, pressing ecological, evolutionary, and conservation biology topics require developing more complex IPMs, and considerably more expertise to implement them. Here, we introduce ipmr, a flexible R package for building, analyzing, and interpreting IPMs. C_LIO_LIThe ipmr framework relies on the mathematical notation of the models to express them in code format. Additionally, this package decouples the model parameterization step from the model implementation step. The latter point substantially increases ipmrs flexibility to model complex life cycles and demographic processes. C_LIO_LIipmr can handle a wide variety of models, including density dependence, discretely and continuously varying stochastic environments, and multiple continuous and/or discrete traits. ipmr can accommodate models with individuals cross-classified by age and size. Furthermore, the package provides methods for demographic analyses (e.g. asymptotic and stochastic growth rates) and visualization (e.g. kernel plotting). C_LIO_LIipmr is a flexible R package for integral projection models. The package substantially reduces the amount of time required to implement general IPMs. We also provide extensive documentation with six vignettes and help files, accessible from an R session and online. C_LI

ecology↗

bioRxiv2021

To buffer or to be labile? A framework to disentangle demographic patterns and evolutionary processes

Until recently, natural selection was assumed to reduce temporal fluctuation in vital rates due to its negative effects on population dynamics - the so-called Demographic Buffering Hypothesis (DBH). After several failures to support the DBH in the two decades since it was first posited, an alternative hypothesis was suggested; the Demographic Lability Hypothesis (DLH), where population vital rates should track rather than buffer the environmental conditions. Despite the huge contribution of both hypotheses to comprehend the demographic strategies to cope the environmental stochasticity, it remains unclear if they represent two competing patterns or the extreme ends of a continuum encompassing all demographic strategies. To solve this historical debate, we unify several methods with an integrative theoretical approach where: i) using the sum of stochastic elasticity with respect to mean and variance - a first-order derivative approach - we rank species on a Buffering-Lability (DB-DL) continuum and ii) using the second-order derivative, we examine how vital rates are shaped by natural selection. Our framework, applied to 40 populations of 34 mammals, successfully placed the species on the DB-DL continuum. We could also link the species' position on the DB-DL continuum to their generation time and time to recovery. Moreover, the second-order derivative unveiled that vital rates with lower temporal variation are not necessarily under a strong pressure of stabilizing selection, as predicted by DBH and DLH. Our framework provides an important step towards unifying the different perspectives of DBH and DLH with key evolutionary concepts.

ecology↗

bioRxiv2021

The fast-slow continuum is not the end-game of life history evolution, human or otherwise

Life history human evolution places a strong emphasis on the fast-slow continuum and pace-of-life continuum. Papers in this area frequently make a call for more integrative research to explore the relationships between the fast-slow continuum (population-level variation in traits) and pace-of-life continuum (ditto at the individual level). Here, using high-resolution demographic models from natural populations of 41 modern human populations, and hundreds of non-human animal populations and plant populations, I show that the fast-slow continuum, while of interest to explore variation in human strategies, should not be the sole focus of attention. Using a phylogenetically corrected principal component analysis, I show that other axes of life history variation show great promise. Specifically, understanding of the mechanisms of inter-specific and intra-specific differences in senescence rates in reproduction and survival, and how species respond to stochastic variation, I argue, should become the focus of my interdisciplinary research. The proposed new axis of demographic buffering-lability emerges as an important one to explain over 20% of variation in human and non-human populations. I show that these axes help predict demographic resilience, and also correlates with human nation per capita GDP and population growth rates.

evolutionary biology↗

bioRxiv2020

Demographic analysis of Israeli Carpobrotus populations: management strategies and future directions

Carpobrotus species are harmful invaders to coastal areas throughout the world, particularly in Mediterranean habitats. Demographic models are ideally suited to identify and understand population processes and stages in the life cycle of the species that could be most effectively targeted with management. However, parameterizing these models has been limited by the difficulty in accessing the cliff-side locations where its populations are typically found, as well as accurately measuring the growth and spread individuals, which form large, dense mats. This study uses small unmanned aerial vehicles (UAVs, drones) to collect demographic data and parameterize an Integral Projection Model of an Israeli Carpobrotus population. We validated our data set with ground targets of known size. Through the analysis of asymptotic growth rates and population sensitivities and elasticities, we demonstrate that the population at the study site is demographically stable, and that reducing the survival and growth of the largest individuals would have the greatest effect on reducing overall population growth rate. Our results provide a first evaluation of the demography of Carpobrotus, a species of conservation and economic concern, and provide the first stage-based population model of a representative of the Aizoaceae family, thus contributing to our global knowledge on plant population dynamics. In addition, we demonstrate the advantages of using drones for collecting demographic data in understudied habitats such as coastal ecosystems.

ecology↗

bioRxiv2020

What are the demographic consequences of a seed bank stage for columnar cacti?

The dynamics of plants populations are often limited by the early stages in their life cycles. The question if the columnar cacti have or not a seed bank in predictable environments. Yet, information regarding seed bank dynamics and how these may influence the full life cycle of plant species is remarkably scarce or ignore. This lack of knowledge is mostly due to the challenges in quantifying seed vital rates. Studies of arid land plant species have historically been focused on the drivers of sporadic recruitment. However, little attention has been given to the demographic consequences of early developmental stages, including seed banks. Here, we evaluate the effects of seed bank survival and seedling recruitment vital rates on the population dynamics and viability of 12 columnar cacti species, recent evidence suggests that cacti seeds may remain viable for the short-term. We assess how changes in the vital rates of these processes, and the inclusion of a seed bank affect population growth rate ({lambda}). We found that a seed bank in the examined matrix population models significantly increased{lambda} as well as the vital rate elasticities of{lambda} to growth and fecundity, whereas that of overall survival decreased. Our numerical simulations showed that seed survival had a larger effect on{lambda} than seedling recruitment and establishment. We suggest that seed bank may explain the structure and population dynamics. Thus, we argue reconsider that this early stage in demographic models will generate more informed decisions on the conservation and management of columnar cacti.

ecology↗

bioRxiv2020

Mapping extinction risk in the global functional spectra across the tree of life

Although one quarter of the species of plants and vertebrates are threatened with extinction, little is known about how the potential effect of extinctions on the global diversity of ecological strategies. Using trait and phylogenetic information for more than 75,000 species of plants, mammals, birds, reptiles, amphibians and freshwater fishes, we characterized the global functional spectra of each of these groups. Mapping of extinction risk within these spectra revealed that larger species with slower pace of life are universally threatened. Simulated potential extinctions revealed extensive internal reorganizations in the global functional spectra, which are particularly severe for mammals and amphibians. Considering the disproportionate importance of the largest species for ecological processes, our results emphasize the importance of actions to prevent the extinction of the megabiota.Competing Interest StatementThe authors have declared no competing interest.View Full Text

ecology↗

bioRxiv2020

Short-lived plants have stronger demographic responses to climate

To mitigate and adapt to climate change, there is an urgent need to synthesize the state of our knowledge on plant responses to climate. The availability of open-access data, combined with our understanding of plant physiology and life history theory provide opportunities to examine quantitative generalizations regarding which biomes and species are most responsive to climate drivers. Here, we synthesized time series of structured population models from 165 populations from 62 plants around the globe to link plant population growth rates to precipitation and temperature drivers. We expected: (1) more pronounced demographic responses to precipitation than temperature, especially in arid biomes; (2) a higher climate sensitivity in short-lived rather than long-lived species; and (3) a stronger response to climate by species that reproduce more frequently. We found that precipitation anomalies have a nearly three-fold larger effect on{lambda} than temperature. Precipitation has substantially more pronounced effects in more arid sites, but large noise makes this relationship non-significant. Species with shorter generation time have much stronger absolute responses to climate anomalies, while the degree of iteroparity does not correlate with population responses to climate. We conclude that key species-level traits can predict plant population responses to climate, and discuss the relevance of this generalization for conservation planning and evolutionary theory.

ecology↗

bioRxiv2020

The demographic buffering strategy has a threshold of effectiveness to increases in environmental stochasticity

O_LIAnimal populations have developed multiple strategies to deal with environmental change. Among them, the demographic buffering strategy consists on constraining the temporal variation of the vital rate(s) (e.g., survival, growth, reproduction) that most affect(s) the overall performance of the population. Given the increase in environmental stochasticity of the current global change scenario, identifying the thresholds beyond which populations are not able to remain viable -despite their potential buffering strategies- is of utmost importance. C_LIO_LITortoises are known to buffer the temporal variation in survival (i.e. this vital rate has the highest contribution to the population growth rate{lambda} ) at the expense of a high variability on reproductive rates (lowest contribution to{lambda} ). To identify the potential threshold in buffering ability, here we use field data collected across a decade on 15 locations of Testudo graeca along South-Eastern Spain. We analyse the effects of environmental variables (precipitation, temperature, and NDVI) on the probability of laying eggs and the number of eggs per clutch. Finally, we couple the demographic and environmental data to parametrise integral projection models (IPMs) to simulate the effects of different scenarios of drought recurrence on population growth rate. C_LIO_LIWe find that droughts negatively affect the probability of laying eggs, but the overall effects on the population growth rates of T. graeca under the current drought frequencies (one per decade) are negligible. However, increasing the annual frequency of droughts decreases the buffering ability of T. graeca populations, with a threshold at three droughts per decade. C_LIO_LIAlthough some species may buffer current environmental regimes by carefully orchestrating how their vital rates vary through time, a demographic buffering strategy may alone not warrant population viability in extreme regimes. Our findings support the hypothesis that the buffering strategy indeed has a threshold of effectiveness. Our methodological approach also provides a useful pipeline for ecologists and managers to determine how effective the management of environmental drivers can be for demographically buffering populations, and which scenarios may not provide long-term species persistence. C_LI

ecology↗