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1.
Science ; 381(6665): 1417, 2023 09 29.
Artículo en Inglés | MEDLINE | ID: mdl-37769070

RESUMEN

An orphaned owl's convalescence inspired an ecologist's reflections during COVID-19 lockdown.

2.
J Phycol ; 59(5): 1107-1111, 2023 10.
Artículo en Inglés | MEDLINE | ID: mdl-37578989

RESUMEN

A cryptogenic, invasive-like red macroalga, Chondria tumulosa, was first observed in 2016 forming thick mats on the forereef of Manawai Atoll within Papahanaumokuakea Marine National Monument. Subsequent expeditions revealed an increased abundance of this alga. In 2021, unattached C. tumulosa was observed forming a network of dark, meandering accumulations throughout the atoll's inner lagoon. High-resolution satellite imagery revealed that these accumulations became visible in 2015 (length: ~0.74 km; area: ~0.88 km2 ) and increased 56-fold in length and 115-fold in area by 2021 (length: 41.32 km; area: 101.34 km2 ). An exponential expansion rate of ~16.02 km · y-1 (length), ~44.75 km2 · y-1 (area). This study presents the comprehensive temporal and spatial expansion of C. tumulosa accumulations for Manawai Atoll since its discovery, providing ecologist and resource managers with a proxy to gauge the overall abundance trend of this invasive-like alga.


Asunto(s)
Antozoos , Rhodophyta , Algas Marinas , Animales , Arrecifes de Coral
3.
Nature ; 2023 Feb 24.
Artículo en Inglés | MEDLINE | ID: mdl-36829063
4.
J Anim Ecol ; 92(4): 936-944, 2023 04.
Artículo en Inglés | MEDLINE | ID: mdl-36785976

RESUMEN

Recent technological advances have led to a rapid increase in the collection of capture-recapture data in continuous time. Unlike traditional capture-recapture data, the detection times from these technologies are themselves random variables and analysis of these data, therefore, requires models that properly account for stochasticity in both state transitions and detection times. Despite the ubiquity of continuously collected capture-recapture data, the mathematical concepts needed to fit continuous-time models remain unfamiliar to many ecologists. In this paper, I provide an introduction to continuous-time models, with a focus on multi-state capture-recapture data. After reviewing the basic structure of these models, I describe several variations, including constant parameters, temporal variation in state transition rates and autocorrelation in detections. To aid comprehension, each model is accompanied by code to simulate data and fit the model in Stan. Although the models presented in this guide are only a small subset of the variations that are possible to suit the needs of specific datasets or questions, the concepts and code will hopefully serve as a foundation for future analyses, allowing ecologists to develop new and creative approaches to continuous-time modelling.


Asunto(s)
Ecología , Modelos Teóricos , Animales
7.
Mol Ecol Resour ; 23(7): 1488-1508, 2023 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-35466564

RESUMEN

The field of molecular biology is advancing fast with new powerful technologies, sequencing methods and analysis software being developed constantly. Commonly used tools originally developed for research on humans and model species are now regularly used in ecological and evolutionary research. There is also a growing interest in the causes and consequences of epigenetic variation in natural populations. Studying ecological epigenetics is currently challenging, especially for vertebrate systems, because of the required technical expertise, complications with analyses and interpretation, and limitations in acquiring sufficiently high sample sizes. Importantly, neglecting the limitations of the experimental setup, technology and analyses may affect the reliability and reproducibility, and the extent to which unbiased conclusions can be drawn from these studies. Here, we provide a practical guide for researchers aiming to study DNA methylation variation in wild vertebrates. We review the technical aspects of epigenetic research, concentrating on DNA methylation using bisulfite sequencing, discuss the limitations and possible pitfalls, and how to overcome them through rigid and reproducible data analysis. This review provides a solid foundation for the proper design of epigenetic studies, a clear roadmap on the best practices for correct data analysis and a realistic view on the limitations for studying ecological epigenetics in vertebrates. This review will help researchers studying the ecological and evolutionary implications of epigenetic variation in wild populations.


Asunto(s)
Metilación de ADN , Epigénesis Genética , Animales , Humanos , Reproducibilidad de los Resultados , Vertebrados/genética , Ecología
8.
Nature ; 612(7940): 582, 2022 12.
Artículo en Inglés | MEDLINE | ID: mdl-36510016
9.
Ecol Evol ; 12(9): e9259, 2022 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-36177125

RESUMEN

One of the most challenging endeavors for students is choosing a career path that best fits their interests, wills and skills, and setting their professional goals accordingly. Such decisions are often made from within the culture of academia, in which mentors and peers are mainly familiar with the academic job market and lack the knowledge necessary to consult about other types of careers. We aimed to address this gap for ecology and related fields by creating an engaging and effective tool to help students and professionals to familiarize themselves with the diversity of potential career paths available to ecologists. The tool is an applied card game - the Ecologist's Career Compass - which is provided here freely. The game is played as a trump card game and includes 33 cards, each representing a combination of one of four job-market sectors and one of nine types of positions. Each card indicates the level of seven skill categories required to likely be hired and succeed in the focal position at the focal sector, as well as more specific examples for typical jobs in the focal combination. The information in the game largely relies on input from a global survey we conducted among 315 ecologists from 35 countries. While the challenges faced by early-career ecologists in developing their professional path are substantial and diverse, this game can assist in gaining a broad comparative overview of the whole ecology job market and the skills required to likely excel in different paths. We hope this applied game will act as a conversation starter about the diversity of aspirations and opportunities in ecology classrooms and labs.

10.
Science ; 377(6607): 699-700, 2022 08 12.
Artículo en Inglés | MEDLINE | ID: mdl-35951688

RESUMEN

University of Delaware finding vindicates whistleblowers.


Asunto(s)
Ecología , Mala Conducta Científica , Denuncia de Irregularidades , Culpa , Humanos , Universidades
11.
Toxins (Basel) ; 14(7)2022 07 17.
Artículo en Inglés | MEDLINE | ID: mdl-35878233

RESUMEN

Bites from venomous marine annelid 'bloodworms' (e.g., Glycera spp.) do not appear to have been described in the medical literature despite being seemingly well-known to bait diggers and fishermen. The few laboratory study reports describe their venom composition and physiological effects in vitro to be primarily proteolytic enzymes and neurotoxins apparently used for predation and defense. Herein, we present the report of a symptomatic envenoming suffered by a marine ecologist bitten while performing her field research. The local effects included a rapid onset of pain, swelling, and numbness at the bite site "as if injected with local anesthetic". Additional signs and symptoms appearing over a two-week period were consistent with both delayed venom effects and potentially secondary infection. The late signs and symptoms resolved during a course of antibiotic treatment with doxycycline prescribed as a precaution and lack of resources to consider a wound culture. Comments about annelid bites sporadically appear in the popular literature, especially pertaining to the fishing industry, under names such as 'bait-diggers hand'. While these bites are not known to be dangerously venomous, they seem to produce painful local symptoms and possibly increase the risk of marine bacterial infections that could be associated with more serious outcomes. More cases need to be formally described to better understand the natural history of these types of envenomation.


Asunto(s)
Poliquetos , Mordeduras de Serpientes , Animales , Antivenenos , Femenino , Neurotoxinas , Mordeduras de Serpientes/terapia , Ponzoñas/toxicidad
12.
Endeavour ; 46(1-2): 100814, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35697549

RESUMEN

Recent research about the microbiome points to a picture in which we, humans, are 'living through' nature, and nature itself is living in us. Our bodies are hosting-and depend on-the multiple species that constitute human microbiota. This article will discuss current research on the microbiome through the ideas of Japanese ecologist Imanishi Kinji (1902-1992). First, some of Imanishi's key ideas regarding the world of living beings and multispecies societies are presented. Second, seven types of relationships concerning the human microbiome, human beings, and the environment are explored. Third, inspired by Imanishi's work, this paper develops the idea of dynamic, porous, and complex multispecies societies in which different living beings or species are codependent on others, including microbiota and human beings.


Asunto(s)
Microbiota , Investigación , Humanos , Investigación/clasificación , Investigación/tendencias
13.
Ecology ; 103(9): e3764, 2022 09.
Artículo en Inglés | MEDLINE | ID: mdl-35608560

RESUMEN

In 1949-1951, ecologist Robert H. Whittaker sampled plant community composition at 470 sites in the Siskiyou Mountains (Oregon and California; also known as Klamath or Klamath-Siskiyou Mountains). His primary goal was to develop methods to quantify plant community variation across environmental gradients, following on his seminal work challenging communities as discrete entities. He selected the Siskiyous because of their diverse and endemic-rich flora, which he attributed to geological complexity and an ancient stable climate. He chose sites to span gradients of topography, elevation, geologic substrate, and distance from the coast. He used the frequencies of indicator species in his data to assign sampling locations to positions on the topographic gradient, nested within the elevational and substrate gradients. He originated in this study the concept of diversity partitioning, in which gamma diversity (species richness of a community) equals alpha diversity (species richness in homogeneous sites) times beta diversity (species turnover among sites along gradients). Diversity partitioning subsequently became highly influential and new developments on it continue. Whittaker published his Siskiyou work covering paleohistory, biogeography, floristics, vegetation, gradient analysis, and diversity partitioning in Ecological Monographs in 1960. Discussed in 2 pages of his 60-page monograph, diversity partitioning accounts for >95% of its current >4300 citations. In 2006, we retrieved Whittaker's Siskiyou data in hard copy from the Cornell University archives and entered them in a database. We used these data for multiple published analyses, including some based on (re)sampling the approximate locations of a subset of his sites. Because of the continued interest in diversity partitioning and in historic data sets, here we present his data, including 359 sampling locations and their descriptors and, for each sample, a list of species with their estimated percent cover (herbs and shrubs) and numbers by diameter at breast height (DBH) category (trees). Site descriptors include the approximate location (road, trail, or stream), elevation, topographic aspect, geologic substrate (serpentine, gabbro, or diorite), and dominant woody vegetation of each location. For 111 sites, including the small number chosen to represent the distance-to-coast gradient, we could not locate his data. There are no copyright restrictions and users of these data should cite this data paper in any publications that result from its use. The authors are available for consultations about and collaborations involving the data.


Asunto(s)
Plantas , Árboles , Biodiversidad , Clima , Ambiente , Humanos , Oregon
14.
Ecology ; 103(6): e3683, 2022 06.
Artículo en Inglés | MEDLINE | ID: mdl-35307820

RESUMEN

In metacommunity ecology, a major focus has been on combining observational and analytical approaches to identify the role of critical assembly processes, such as dispersal limitation and environmental filtering, but this work has largely ignored temporal community dynamics. Here, we develop a "virtual ecologist" approach to evaluate assembly processes by simulating metacommunities varying in three main processes: density-independent responses to abiotic conditions, density-dependent biotic interactions, and dispersal. We then calculate a number of commonly used summary statistics of community structure in space and time and use random forests to evaluate their utility for inferring the strength of these three processes. We find that (i) both spatial and temporal data are necessary to disentangle metacommunity processes based on the summary statistics we test, and including statistics that are measured through time increases the explanatory power of random forests by up to 59% compared to cases where only spatial variation is considered; (ii) the three studied processes can be distinguished with different descriptors; and (iii) each summary statistic is differently sensitive to temporal and spatial sampling effort. Including repeated observations of metacommunities over time was essential for inferring the metacommunity processes, particularly dispersal. Some of the most useful statistics include the coefficient of variation of species abundances through time and metrics that incorporate variation in the relative abundances (evenness) of species. We conclude that a combination of methods and summary statistics is probably necessary to understand the processes that underlie metacommunity assembly through space and time, but we recognize that these results will be modified when other processes or summary statistics are used.


Asunto(s)
Biodiversidad , Ecosistema , Ecología
15.
Ecol Evol ; 12(2): e8430, 2022 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-35222942

RESUMEN

The influence of climate on the distribution of taxa has been extensively investigated in the last two decades through Habitat Suitability Models (HSMs). In this context, the Worldclim database represents an invaluable data source as it provides worldwide climate surfaces for both historical and future time horizons. Thousands of HSMs-based papers have been published taking advantage of Worldclim 1.4, the first online version of this repository. In 2017, Worldclim 2.1 was released. Here, we evaluated spatially explicit prediction mismatch at continental scale, focusing on Europe, between HSMs fitted using climate surfaces from the two Worldclim versions (between-version differences). To this aim, we simulated occurrence probability and presence-absence across Europe of four virtual species (VS) with differing climate-occurrence relationships. For each VS, we fitted HSMs upon uncorrelated bioclimatic variables derived from each Worldclim version at three grid resolutions. For each factor combination, HSMs attaining sufficient discrimination performance on spatially independent test data were projected across Europe under current conditions and various future scenarios, and importance scores of the single variables were computed. HSMs failed in accurately retrieving the simulated climate-occurrence relationships for the climate-tolerant VS and the one occurring under a narrow combination of climatic conditions. Under current climate, noticeable between-version prediction mismatch emerged across most of Europe for these two VSs, whose simulated suitability mainly depended upon diurnal or yearly variability in temperature; differently, between-version differences were more clustered toward areas showing extreme values, like mountainous massifs or southern regions, for VSs responding to average temperature and precipitation trends. Under future climate, the chosen emission scenarios and Global Climate Models did not evidently influence between-version prediction discrepancies, while grid resolution synergistically interacted with VSs' niche characteristics in determining extent of such differences. Our findings could help in re-evaluating previous biodiversity-related works relying on geographical predictions from Worldclim-based HSMs.

16.
iScience ; 25(2): 103775, 2022 Feb 18.
Artículo en Inglés | MEDLINE | ID: mdl-35146390

RESUMEN

Understanding the sets of inter- and intraspecies interactions in microbial communities is a fundamental goal of microbial ecology. However, the study and quantification of microbial interactions pose several challenges owing to their complexity, dynamic nature, and the sheer number of unique interactions within a typical community. To overcome such challenges, microbial ecologists must rely on various approaches to distill the system of study to a functional and conceptualizable level, allowing for a practical understanding of microbial interactions in both simplified and complex systems. This review broadly addresses the role of several conceptual approaches available for the microbial ecologist's arsenal, examines specific tools used to accomplish such approaches, and describes how the assumptions, expectations, and philosophies underlying these tools change across scales of complexity.

17.
Anim Biotelemetry ; 10(1): 10, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-37521810

RESUMEN

Background: Recent developments in both hardware and software of animal-borne data loggers now enable large amounts of data to be collected on both animal movement and behaviour. In particular, the combined use of tri-axial accelerometers, tri-axial magnetometers and GPS loggers enables animal tracks to be elucidated using a procedure of 'dead-reckoning'. Although this approach was first suggested 30 years ago by Wilson et al. (1991), surprisingly few measurements have been made in free-ranging terrestrial animals. The current study examines movements, interactions with habitat features, and home-ranges calculated from just GPS data and also from dead-reckoned data in a model terrestrial mammal, the European badger (Meles meles). Methods: Research was undertaken in farmland in Northern Ireland. Two badgers (one male, one female) were live-trapped and fitted with a GPS logger, a tri-axial accelerometer, and a tri-axial magnetometer. Thereafter, the badgers' movement paths over 2 weeks were elucidated using just GPS data and GPS-enabled dead-reckoned data, respectively. Results: Badgers travelled further using data from dead-reckoned calculations than using the data from only GPS data. Whilst once-hourly GPS data could only be represented by straight-line movements between sequential points, the sub-second resolution dead-reckoned tracks were more tortuous. Although there were no differences in Minimum Convex Polygon determinations between GPS- and dead-reckoned data, Kernel Utilisation Distribution determinations of home-range size were larger using the former method. This was because dead-reckoned data more accurately described the particular parts of landscape constituting most-visited core areas, effectively narrowing the calculation of habitat use. Finally, the dead-reckoned data showed badgers spent more time near to field margins and hedges than simple GPS data would suggest. Conclusion: Significant differences emerge when analyses of habitat use and movements are compared between calculations made using just GPS data or GPS-enabled dead-reckoned data. In particular, use of dead-reckoned data showed that animals moved 2.2 times farther, had better-defined use of the habitat (revealing clear core areas), and made more use of certain habitats (field margins, hedges). Use of dead-reckoning to provide detailed accounts of animal movement and highlight the minutiae of interactions with the environment should be considered an important technique in the ecologist's toolkit.

18.
Glob Chang Biol ; 28(2): 665-684, 2022 01.
Artículo en Inglés | MEDLINE | ID: mdl-34543495

RESUMEN

Terrestrial ecosystems regulate Earth's climate through water, energy, and biogeochemical transformations. Despite a key role in regulating the Earth system, terrestrial ecology has historically been underrepresented in the Earth system models (ESMs) that are used to understand and project global environmental change. Ecology and Earth system modeling must be integrated for scientists to fully comprehend the role of ecological systems in driving and responding to global change. Ecological insights can improve ESM realism and reduce process uncertainty, while ESMs offer ecologists an opportunity to broadly test ecological theory and increase the impact of their work by scaling concepts through time and space. Despite this mutualism, meaningfully integrating the two remains a persistent challenge, in part because of logistical obstacles in translating processes into mathematical formulas and identifying ways to integrate new theories and code into large, complex model structures. To help overcome this interdisciplinary challenge, we present a framework consisting of a series of interconnected stages for integrating a new ecological process or insight into an ESM. First, we highlight the multiple ways that ecological observations and modeling iteratively strengthen one another, dispelling the illusion that the ecologist's role ends with initial provision of data. Second, we show that many valuable insights, products, and theoretical developments are produced through sustained interdisciplinary collaborations between empiricists and modelers, regardless of eventual inclusion of a process in an ESM. Finally, we provide concrete actions and resources to facilitate learning and collaboration at every stage of data-model integration. This framework will create synergies that will transform our understanding of ecology within the Earth system, ultimately improving our understanding of global environmental change, and broadening the impact of ecological research.


Asunto(s)
Planeta Tierra , Ecosistema , Ecología , Incertidumbre , Agua
19.
Microb Ecol ; 84(1): 182-197, 2022 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-34406445

RESUMEN

Keystone species or ecological engineers are vital to the health of an ecosystem; however, often, their low abundance or biomass present challenges for their discovery, identification, visualization and selection. We report the development of fluorescent in situ hybridization of transcript-annealing molecular beacons (FISH-TAMB), a fixation-free protocol that is applicable to archaea and bacteria. The FISH-TAMB method differs from existing FISH methods by the absence of fixatives or surfactants in buffers, the fast hybridization time of as short as 15 min at target cells' growth temperature, and the omission of washing steps. Polyarginine cell-penetrating peptides are employed to deliver molecular beacons (MBs) across prokaryotic cell walls and membranes, fluorescently labeling cells when MBs hybridize to target mRNA sequences. Here, the detailed protocol of the preparation and application of FISH-TAMB is presented. To demonstrate FISH-TAMB's ability to label intracellular mRNA targets, differentiate transcriptional states, detect active and rare taxa, and keep cell viability, labeling experiments were performed that targeted the messenger RNA (mRNA) of methyl-coenzyme M reductase A (mcrA) expressed in (1) Escherichia coli containing a plasmid with a partial mcrA gene of the methanogen Methanosarcina barkeri (E. coli mcrA+); (2) M. barkeri; and (3) an anaerobic methanotrophic (ANME) enrichment from a deep continental borehole. Although FISH-TAMB was initially envisioned for mRNA of any functional gene of interest without a requirement of prior knowledge of 16S ribosomal RNA (rRNA)-based taxonomy, FISH-TAMB has the potential for multiplexing and going beyond mRNA and thus is a versatile addition to the molecular ecologist's toolkit, with potentially widespread application in the field of environmental microbiology.


Asunto(s)
Metano , Microbiota , Archaea , ADN de Archaea/genética , Escherichia coli/genética , Hibridación Fluorescente in Situ/métodos , Metano/metabolismo , Oxidorreductasas/genética , Filogenia , ARN Mensajero/genética , ARN Mensajero/metabolismo , ARN Ribosómico 16S/genética , ARN Ribosómico 16S/metabolismo
20.
J Theor Biol ; 534: 110976, 2022 02 07.
Artículo en Inglés | MEDLINE | ID: mdl-34883120

RESUMEN

Using spatialised population measurements and related geographic habitat data, it is feasible nowadays to derive parsimonious spatially explicit population models and to carry on their parameter estimation. To achieve such goal, reaction-diffusion models are common in conservation biology and agricultural plant health where they are used, for example, for landscape planning or epidemiological surveillance. Unfortunately, if the mathematical methods and computational power are readily available, biological measurements are not. Despite the high throughput of some habitat related remote sensors, the experimental cost of biological measurements are one of the worst bottleneck against a widespread usage of reaction-diffusion models. Hence we will recall some classical methods for optimal experimental design that we deem useful to spatial ecologist. Using two case studies, one in landscape ecology and one in conservation biology, we will show how to construct a priori experimental design minimizing variance of parameter estimates, enabling optimal experimental setup under constraints.


Asunto(s)
Ecosistema , Plantas , Difusión , Modelos Biológicos , Dinámica Poblacional
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