Data from: Maladaptation beyond a geographic range limit driven by antagonistic and mutualistic biotic interactions across an abiotic gradient
Contributors: Benning, John William, Moeller, David
... Species’ geographic range limits often result from maladaptation to the novel environments beyond the range margin. However, we rarely know which aspects of the n-dimensional environment are driving this maladaptation. Especially of interest is the influence of abiotic versus biotic factors in delimiting species’ distributions. We conducted a two-year reciprocal transplant experiment involving manipulations of the biotic environment to explore how spatio-temporal gradients in precipitation, fatal mammalian herbivory, and pollination affected lifetime fitness within and beyond the range of the California annual plant, Clarkia xantiana ssp. xantiana. In the first, drier year of the experiment, fitness outside the range edge was limited mainly by low precipitation, and there was some evidence for local adaptation within the range. In the second, wetter year, we did not observe abiotic limitations to plant fitness outside the range; instead biotic interactions, especially herbivory, limited fitness outside the range. Together, protection from herbivory and supplementation of pollen resulted in 3-7 fold increases in lifetime fitness outside the range margin in the abiotically benign year. Overall, our work demonstrates the importance of biotic interactions, particularly as they interact with the abiotic environment, in determining fitness beyond geographic range boundaries.
Contributors: Sinn, Brandon T, Barrett, Craig F
... The mitochondrial genomes (mitogenomes) of plants are known to incorporate and accumulate DNA from intra- and extracellular donors. Despite the intimate relationships formed between flowing plants (angiosperms) and fungi, lengthy fungal-like sequence has not been identified in angiosperm mitogenomes to date. Here we present multiple lines of evidence documenting horizontal gene transfer (HGT) between the mitogenomes of fungi and the ancestors of the orchids, plants that are obligate parasites of fungi during their early development. We show that the ancestor of the orchids acquired an approximately 270 bp fungal mitogenomic region containing three transfer RNA genes. We propose that the short HGT was later replaced by a second HGT event transferring more than 8 kb and 14 genes from a fungal mitogenome to that of the ancestor of the largest orchid subfamily, Epidendroideae. Our results represent the first evidence of genomic-scale HGT between fungal and angiosperm mitogenomes and demonstrate that the length intergenic spacer regions of angiosperm mitogenomes can effectively fossilize the genomic remains of ancient, non-plant organisms.
Data from: Hierarchical controls on extinction selectivity across the diplobathrid crinoid phylogeny
Contributors: Cole, Selina
... Identifying correlates of extinction risk is important for understanding the underlying mechanisms driving differential rates of extinction and variability in the temporal durations of taxa. Increasingly, it is recognized that the effects of multiple, potentially interacting variables and phylogenetic relationships should be incorporated when studying extinction selectivity to account for covariation of traits and shared evolutionary history. Here, I explore a variety of biological and ecological controls on genus longevity in the global fossil record of diplobathrid crinoids by analyzing the combined effects of species richness, habitat preference, body size, filtration fan density, and food size selectivity. I employ a suite of taxic and phylogenetic approaches to (1) quantitatively compare and rank the relative effects of multiple factors on taxonomic longevity, and (2) determine how phylogenetic comparative approaches alter interpretations of extinction selectivity. I find controls on diplobathrid genus duration are hierarchically structured, where species richness is the primary predictor of duration, habitat is the secondary predictor, and a combination of ecological and biological traits are tertiary controls. Ecology plays an important but complex role in the generation of crinoid macroevolutionary patterns. Notably, tolerance of environmental heterogeneity promotes increased genus duration across diplobathrid crinoids, and the effects of traits related to feeding ecology vary depending on habitat lithology. Finally, I find accounting for phylogeny does not consistently decrease the significance of correlations between traits and genus duration, as is commonly expected. Instead, the strength of relationships between traits and duration may increase, decrease, or remain statistically similar, and both the magnitude and direction of these shifts are generally unpredictable. However, traits with strong correlations and/or moderately large effect sizes (Cohen’s f2 > 0.15) under taxic approaches tend to remain qualitatively unchanged under phylogenetic approaches.
Top results from Data Repository sources. Show only results like these.
Contributors: Kefi, Sonia, Dominguez-Garcia, Virginia, Donohue, Ian, Fontaine, Colin, Thébault, Elisa, Dakos, Vasilis
... The concept of ecological stability occupies a prominent place in both fundamental and applied ecological research. We review decades of work on the topic and examine how our understanding has progressed. We show that our understanding of stability has remained fragmented and is limited largely to simple or simplified systems. There has been a profusion of metrics proposed to quantify stability, of which only a handful are used commonly. Furthermore, studies typically quantify one to two metrics of stability at a time and in response to a single perturbation, with some of the main environmental pressures of today being the least studied. We argue that we need to build on the existing consensus and strong theoretical foundation of the stability concept to better understand its multidimensionality and the interdependencies between metrics, levels of organization and types of perturbations. Only by doing so can we make progress in the quantification of stability in theory and in practice and eventually build a more comprehensive understanding of how ecosystems will respond to ongoing environmental change.
Contributors: Shores, Carolyn R., Dellinger, Justin A., Newkirk, Eric S., Kachel, Shannon M., Wirsing, Aaron J.
... Apex predators can influence ecosystems through density and behaviorally mediated effects on herbivores and mesopredators. In many parts of the world, apex predators live in, or are returning to, landscapes that have been modified by people, so it is important to understand their ecological role in anthropogenic landscapes. We used motion-activated game cameras to compare the activity patterns of humans and two mesopredators, coyotes (Canis latrans) and bobcats (Lynx rufus), in areas with and without an apex predator, the gray wolf (Canis lupus), in a multi-use landscape of the northwestern United States. In areas with wolves there was a significant increase in temporal niche overlap between the mesopredators owing to higher levels of coyote activity at all time periods of the day. Temporal overlap between mesopredators and humans also increased significantly in the presence of wolves. Coyotes exposed to wolves increased their activity during dawn, day, and dusk hours. The increase in coyote activity was greatest during the day, when wolves were least active. The direction of change in bobcat activity in areas with wolves was opposite to coyotes, suggesting a behaviorally-mediated cascade between wolves, coyotes, and bobcats, although these findings would need to be confirmed with further research. Our findings suggest that mesopredators in human-dominated systems may perceive humans as less dangerous than apex predators, that humans may be more likely to encounter mesopredators in areas occupied by top predators, and that behaviorally-mediated effects of apex predators on mesopredators persist in human-dominated landscapes.
Data from: Dense geographic and genomic sampling reveals paraphyly and a cryptic lineage in a classic sibling species complex
Contributors: Linck, Ethan, Epperly, Kevin, van Els, Paul, Spellman, Garth, Bryson, Rob, McCormack, John, Canales-del-Castillo, Ricardo, Klicka, John
... Incomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis / E. occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of widely-distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or “sibling”) lineages following extensive study. Though the group is well-characterized north of the U.S. Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this paper, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis / E . occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the group’s range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E. difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution.
Data from: Pollen on stigmas of herbarium specimens: a window into the impacts of a century of environmental disturbance on pollen transfer
Contributors: Johnson, Anna L., Rebolleda-Gomez, Maria, Ashman, Tia Lynn
... Pollination is necessary for plant reproduction, but often highly susceptible to disruption, e.g., by habitat fragmentation and climate change. Here, we evaluated on a century time scale pollination interactions for species in one of the historically most disturbed habitats on earth-- tropical dry forests of Hawai’i. We employed a novel method for acquiring a historical perspective on temporal change in pollination by characterizing pollen on stigmas of herbarium specimens from six remnant native species collected from 1909-2002. We determine whether temporal shifts occurred in 1) pollination quantity and quality, or 2) the composition of species interacting via pollen transfer. While pollen quantity remained constant, these remnant species interact with different species in modern times via pollen transfer than they did nearly 100 years ago. Species which are resilient to long-term environmental change may also be the ones subject to changes in pollination interactions.
Data from: Automated peak detection method for behavioral event identification: detecting Balaenoptera musculus and Grampus griseus feeding attempts
Contributors: Sweeney, David A., DeRuiter, Stacy L., McNamara-Oh, Ye Joo, Marques, Tiago A., Arranz, Patricia, Calambokidis, John
... The desire of animal behaviorists for more flexible methods of conducting inter-study and inter-specific comparisons and meta-analysis of various animal behaviors compelled us to design an automated, animal behavior peak detection method that is potentially generalizable to a wide variety of data types, animals, and behaviors. We detected the times of feeding attempts by 12 Risso’s dolphins (Grampus griseus) and 36 blue whales (Balaenoptera musculus) using the norm-jerk (rate of change of acceleration) time series. The automated peak detection algorithm identified median true-positive rates of 0.881 for blue whale lunges and 0.410 for Risso’s dolphin prey capture attempts, with median false-positive rates of 0.096 and 0.007 and median miss rates of 0.113 and 0.314, respectively. Our study demonstrates that our peak detection method is efficient at automatically detecting animal behaviors from multisensor tag data with high accuracy for behaviors that are appropriately characterized by the data time series.
Data from: Assimilating MODIS data-derived minimum input data set and water stress factors into CERES-Maize model improves regional corn yield predictions
Contributors: Ban, Ho-Young, Ahn, Joong-Bae, Lee, Byun-Woo
... Crop growth models and remote sensing are useful tools for predicting crop growth and yield, but each tool has inherent drawbacks when predicting crop growth and yield at a regional scale. To improve the accuracy and precision of regional corn yield predictions, a simple approach for assimilating Moderate Resolution Imaging Spectroradiometer (MODIS) products into a crop growth model was developed, and regional yield prediction performance was evaluated in a major corn-producing state, Illinois, USA. Corn growth and yield were simulated for each grid using the Crop Environment Resource Synthesis (CERES)-Maize model with minimum inputs comprising planting date, fertilizer amount, genetic coefficients, soil, and weather data. Planting date was estimated using a phenology model with a leaf area duration (LAD)-logistic function that describes the seasonal evolution of MODIS-derived leaf area index (LAI). Genetic coefficients of the corn cultivar were determined to be the genetic coefficients of the maturity group [included in Decision Support System for Agrotechnology Transfer (DSSAT) 4.6], which shows the minimum difference between the maximum LAI derived from the LAD-logistic function and that simulated by the CERES-Maize model. In addition, the daily water stress factors were estimated from the ratio between daily leaf area/weight growth rates estimated from the LAD-logistic function and that simulated by the CERES-Maize model under the rain-fed and auto-irrigation conditions. The additional assimilation of MODIS data-derived water stress factors and LAI under the auto-irrigation condition showed the highest prediction accuracy and precision for the yearly corn yield prediction (R2 is 0.78 and the root mean square error is 0.75 t ha-1). The present strategy for assimilating MODIS data into a crop growth model using minimum inputs was successful for predicting regional yields, and it should be examined for spatial portability to diverse agro-climatic and agro-technology regions.
Data from: Ecological and spatial patterns associated with diversification of the shrub genus Tetraglochin along Southern-Central Andes (Rosaceae)
Contributors: Salariato, Diego Leonel, Acosta, Juan Manuel, Cialdella, Ana María
... In addition to the degree of geographical isolation (sympatry, parapatry, allopatry and peripatry), ecology can be an important factor promoting diversification of lineages, both by niche divergence as well as niche conservatism. Tetraglochin is a genus of shrubs with six species distributed along the Southern and Central Andes, from Peru to southern Argentina and central Chile. Although monophyly of the genus as the identity of its species are well established, spatiotemporal framework for its diversification and the potential role of the ecology and geography in the speciation process remain unknown. In the present study we analyzed diversification times and historical biogeography of the genus, and conducted different climatic niche and geographical range comparisons among its species to determine possible patterns associated with speciation. Results support the Pleistocene diversification, early along the Southern Andes and the Patagonian Steppe and subsequently in the Central Andes. Climatic niche divergence did not prove to be a major factor promoting speciation, but rather the phylogenetic niche conservatism. Our analyses also favored the sympatric model of speciation, although patterns from geographical range evolution are difficult to interpret due to the lability on the ancestral distributions, and therefore micro-allopatric or parapatric divergence associated with the glacial-interglacial cycles and climatic oscillations throughout the Quaternary should not be discarded. Other potential factors associated with diversification of Tetraglochin are also discussed.