Dataset Information

Spatial Phylogenetics of Florida Vascular Plants: The Effects of Calibration and Uncertainty on Diversity Estimates.

ABSTRACT: Recent availability of biodiversity data resources has enabled an unprecedented ability to estimate phylogenetically based biodiversity metrics over broad scales. Such approaches elucidate ecological and evolutionary processes yielding a biota and help guide conservation efforts. However, the choice of appropriate phylogenetic resources and underlying input data uncertainties may affect interpretation. Here, we address how differences among phylogenetic source trees and levels of phylogenetic uncertainty affect these metrics and test existing hypotheses regarding geographic biodiversity patterns across the diverse vascular plant flora of Florida, US. Ecological niche models for 1,490 Florida species were combined with a "purpose-built" phylogenetic tree (phylogram and chronogram), as well as with trees derived from community resources (Phylomatic and Open Tree of Life). There were only modest differences in phylodiversity metrics given the phylogenetic source tree and taking into account the level of phylogenetic uncertainty; we identify similar areas of conservation interest across Florida regardless of the method used.

SUBMITTER: Allen JM

PROVIDER: S-EPMC6308250 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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Publications

Spatial Phylogenetics of Florida Vascular Plants: The Effects of Calibration and Uncertainty on Diversity Estimates.

Allen Julie M JM Germain-Aubrey Charlotte C CC Barve Narayani N Neubig Kurt M KM Majure Lucas C LC Laffan Shawn W SW Mishler Brent D BD Owens Hannah L HL Smith Stephen A SA Whitten W Mark WM Abbott J Richard JR Soltis Douglas E DE Guralnick Robert R Soltis Pamela S PS

iScience 20181208

Recent availability of biodiversity data resources has enabled an unprecedented ability to estimate phylogenetically based biodiversity metrics over broad scales. Such approaches elucidate ecological and evolutionary processes yielding a biota and help guide conservation efforts. However, the choice of appropriate phylogenetic resources and underlying input data uncertainties may affect interpretation. Here, we address how differences among phylogenetic source trees and levels of phylogenetic un ...[more]

PMID: 30590251

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Project description:We report continuous surface observations of carbon dioxide (CO2) and methane (CH4) from the Los Angeles (LA) Megacity Carbon Project during 2015. We devised a calibration strategy, methods for selection of background air masses, calculation of urban enhancements, and a detailed algorithm for estimating uncertainties in urban-scale CO2 and CH4 measurements. These methods are essential for understanding carbon fluxes from the LA megacity and other complex urban environments globally. We estimate background mole fractions entering LA using observations from four "extra-urban" sites including two "marine" sites located south of LA in La Jolla (LJO) and offshore on San Clemente Island (SCI), one "continental" site located in Victorville (VIC), in the high desert northeast of LA, and one "continental/mid-troposphere" site located on Mount Wilson (MWO) in the San Gabriel Mountains. We find that a local marine background can be established to within ~1 ppm CO2 and ~10 ppb CH4 using these local measurement sites. Overall, atmospheric carbon dioxide and methane levels are highly variable across Los Angeles. "Urban" and "suburban" sites show moderate to large CO2 and CH4 enhancements relative to a marine background estimate. The USC (University of Southern California) site near downtown LA exhibits median hourly enhancements of ~20 ppm CO2 and ~150 ppb CH4 during 2015 as well as ~15 ppm CO2 and ~80 ppb CH4 during mid-afternoon hours (12:00-16:00 LT, local time), which is the typical period of focus for flux inversions. The estimated measurement uncertainty is typically better than 0.1 ppm CO2 and 1 ppb CH4 based on the repeated standard gas measurements from the LA sites during the last 2 years, similar to Andrews et al. (2014). The largest component of the measurement uncertainty is due to the single-point calibration method; however, the uncertainty in the background mole fraction is much larger than the measurement uncertainty. The background uncertainty for the marine background estimate is ~10 and ~15 % of the median mid-afternoon enhancement near downtown LA for CO2 and CH4, respectively. Overall, analytical and background uncertainties are small relative to the local CO2 and CH4 enhancements; however, our results suggest that reducing the uncertainty to less than 5 % of the median mid-afternoon enhancement will require detailed assessment of the impact of meteorology on background conditions.

Project description:BackgroundConservation practitioners are often interested in developing land use plans that increase landscape connectivity, which is defined as the degree to which the landscape facilitates or impedes movement among resource patches. Landscape connectivity is often estimated with a cost surface that indicates the varying costs experienced by an organism in moving across a landscape. True, or absolute costs are rarely known however, and therefore assigning costs to different landscape elements is often a challenge in creating cost surface maps. As such, we consider it important to understand the sensitivity of connectivity estimates to uncertainty in cost estimates.MethodsWe used simulated landscapes to test the sensitivity of current density estimates from circuit theory to varying relative cost values, fragmentation, and number of cost classes (i.e., thematic resolution). Current density is proportional to the probability of use during a random walk. Using Circuitscape software, we simulated electrical current between pairs of nodes to create current density maps. We then measured the correlation of the current density values across scenarios.ResultsIn general, we found that cost values were highly correlated across scenarios with different cost weights (mean correlation ranged from 0.87 to 0.92). Changing the spatial configuration of landscape elements by varying the degree of fragmentation reduced correlation in current density across maps. We also found that correlations were more variable when the range of cost values in a map was high.DiscussionThe low sensitivity of current density estimates to relative cost weights suggests that the measure may be reliable for land use applications even when there is uncertainty about absolute cost values, provided that the user has the costs correctly ranked. This finding should facilitate the use of cost surfaces by conservation practitioners interested in estimating connectivity and planning linkages and corridors.

Dataset Information

Spatial Phylogenetics of Florida Vascular Plants: The Effects of Calibration and Uncertainty on Diversity Estimates.

Publications

Spatial Phylogenetics of Florida Vascular Plants: The Effects of Calibration and Uncertainty on Diversity Estimates.

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