Contributors: Detto, Matteo, Visser, Marco D., Wright, S. J., Pacala, Stephen W.
... Regression dilution is a statistical inference bias that causes underestimation of the strength of dependency between two variables when the predictors are error-prone proxies (EPPs). EPPs are widely used in plant community studies focused on negative density-dependence (NDD) to quantify competitive interactions. Because of the nature of the bias, conspecific NDD is often overestimated in recruitment analyses, and in some cases, can be erroneously detected when absent. In contrast, for survival analyses, EPPs typically cause NDD to be underestimated, but underestimation is more severe for abundant species and for heterospecific effects, thereby generating spurious negative relationships between the strength of NDD and the abundances of con- and heterospecifics. This can explain why many studies observed rare species to suffer more severely from conspecific NDD, and heterospecific effects to be disproportionally smaller than conspecific effects. In general, such species-dependent bias is often related to traits associated with likely mechanisms of NDD, which creates false patterns and complicates the ecological interpretation of the analyses. Classic examples taken from literature and simulations demonstrate that this bias has been pervasive, which calls into question the emerging paradigm that intraspecific competition has been demonstrated by direct field measurements to be generally stronger than interspecific competition.
Contributors: Graves, Gary R.
... NH-Vertebrate Zoology
Calculation of narrower confidence intervals for tree mortality rates when we know nothing but the location of the death/survival events
Contributors: Arellano, Gabriel
... Many ecological applications, like the study of mortality rates, require the estimation of proportions and confidence intervals for them. The traditional way of doing this applies the binomial distribution, which describes the outcome of a series of Bernoulli trials. This distribution assumes that observations are independent and the probability of success is the same for all the individual observations. Both assumptions are obviously false in many cases. I show how to apply bootstrap and the Poisson binomial distribution (a generalization of the binomial distribution) to the estimation of proportions. Any information at the individual level would result in better (narrower) confidence intervals around the estimation of proportions. As a case study, I applied this method to the calculation of mortality rates in a forest plot of tropical trees in Lambir Hills National Park, Malaysia. I calculated central estimates and 95% confidence intervals for species-level mortality rates for 1,007 tree species. I used a very simple model of spatial dependence in survival to estimate individual-level risk of mortality. The results obtained by accounting for heterogeneity in individual-level risk of mortality were comparable to those obtained with the binomial distribution in terms of central estimates, but the precision increased in virtually all cases, with an average reduction in the width of the confidence interval of 20%. Spatial information allows the estimation of individual-level probabilities of survival, and this increases the precision in the estimates of mortality rates. The general method described here, with modifications, could be applied to reduce uncertainty in the estimation of proportions related to any spatially structured phenomenon with two possible outcomes. More sophisticated approaches can yield better estimates of individual-level mortality and thus narrower confidence intervals.
Borealodon osedax, a new stem mysticete (Mammalia, Cetacea) from the Oligocene of Washington State and its implications for fossil whale-fall communities
Contributors: Shipps, B. K., Peredo, Carlos Mauricio, Pyenson, Nicholas D.
... Baleen whales (mysticetes) lack teeth as adults and instead filter feed using keratinous baleen plates. They do not echolocate with ultrasonic frequencies like toothed whales but are instead known for infrasonic acoustics. Both baleen and infrasonic hearing are separately considered key innovations linked to their gigantism, evolutionary success and ecological diversity. The earliest mysticetes had teeth, and the phylogenetic position of many so-called toothed mysticetes remains debated, including those belonging to the nominal taxonomic groups Llanocetidae, Mammalodontidae and Aetiocetidae. Here, we report a new stem mysticete, Borealodon osedax gen. et sp. nov., from the Oligocene of Washington State, USA. Borealodon preserves multi-cusped teeth with apical wear; microCT scans of the inner ear indicate that the minimum frequency hearing limit of Borealodon was similar to mammalodontids. Borealodon is not recovered within a monophyletic Mammalodontidae nor a monophyletic Aetiocetidae; instead, it represents an unnamed lineage of stem Mysticeti, adding to the diversity of stem mysticetes, especially across the Rupelian-Chattian boundary. Furthermore, the presence of a putative chemosynthetic bivalve along with Osedax, a bone-boring annelid, found in association with the type specimen of Borealodon, offer more insights into the evolution of deep-sea whale-fall communities.
Contributors: Heckadon-Moreno, Stanley
Quantifying Leaf Phenology of Individual Trees and Species in a Tropical Forest Using Unmanned Aerial Vehicle (UAV) Images
Contributors: Park, John Y., Muller-Landau, Helene, Lichstein, Jeremy W., Rifai, Sami W., Dandois, Jonathan P., Bohlman, Stephanie A.
... Tropical forests exhibit complex but poorly understood patterns of leaf phenology. Understanding species- and individual-level phenological patterns in tropical forests requires datasets covering large numbers of trees, which can be provided by Unmanned Aerial Vehicles (UAVs). In this paper, we test a workflow combining high-resolution RGB images (7 cm/pixel) acquired from UAVs with a machine learning algorithm to monitor tree and species leaf phenology in a tropical forest in Panama. We acquired images for 34 flight dates over a 12-month period. Crown boundaries were digitized in images and linked with forest inventory data to identify species. We evaluated predictions of leaf cover from different models that included up to 14 image features extracted for each crown on each date. The models were trained and tested with visual estimates of leaf cover from 2422 images from 85 crowns belonging to eight species spanning a range of phenological patterns. The best-performing model included both standard color metrics, as well as texture metrics that quantify within-crown variation, with r2 of 0.84 and mean absolute error (MAE) of 7.8% in 10-fold cross-validation. In contrast, the model based only on the widely-used Green Chromatic Coordinate (GCC) index performed relatively poorly (r2 = 0.52, MAE = 13.6%). These results highlight the utility of texture features for image analysis of tropical forest canopies, where illumination changes may diminish the utility of color indices, such as GCC. The algorithm successfully predicted both individual-tree and species patterns, with mean r2 of 0.82 and 0.89 and mean MAE of 8.1% and 6.0% for individual- and species-level analyses, respectively. Our study is the first to develop and test methods for landscape-scale UAV monitoring of individual trees and species in diverse tropical forests. Our analyses revealed undescribed patterns of high intraspecific variation and complex leaf cover changes for some species.
Chemical Profiling of Volatile Components of the Gametophyte and Sporophyte Stages of the Hornwort Leiosporoceros dussii (Leiosporocerotaceae) From Panama by HS-SPME-GC-MS
Contributors: Garrido, Anette, Gudiño Ledezma, José, Durant-Archibold, Armando, Salazar Allen, Noris, Juan, Villarreal A.,, Gupta, Mahabir P.
... We report for the first time the chemical profiling of volatile organic compounds (VOCs) of gametophyte and sporophyte life stages of Leiosporoceros dussii, from Panama by using headspace-solid phase microextraction-gas chromatography-mass spectrometry in order to assess distinguishing chemical markers between the male and female gametophytes, and sporophytes of this hornwort. A total of 27 VOCs were identified in L. dussii. Furthermore, the gametophyte and sporophyte showed clear differences in the type and amount of VOCs. The main constituents of L. dussii female thalli were menthacamphor (17.8%), hexanol (12.3%), and menthyl acetate (12.3%), while the major compounds of the male thalli were hexanol (25.3%), ß-ionone (21.1%), benzeneacetaldehyde (17.6%), and ß-cyclocitral (14.0%). The main VOCs of the sporophytes were hexanal (19.3%), ß-cyclocitral (17.6%), 2-nonenal (15.8%), hexanol (12.5%), and ß-ionone (10.2%). Unique compounds found in the female thalli were 3-pentanone, 3-octenol, nonanol, estragole, and menthyl acetate, and in the male thalli were methyl heptenone, nonanal, neoisomenthol, and bornyl acetate. Isomenthol, thymol, isomenthol acetate, and ß-methylnaphthalene were only found in the sporophyte. The characteristic VOCs identified in L. dussii suggest a difference between the chemical constituents of L. dussii and other hornworts species. The presence of simple VOCs when compared with compounds previously characterized in another hornwort genera may support the distinct genetic nature of this species.
Contributors: Choi, Bokyung, Crisp, Michael D., Cook, Lyn G., Meusemann, Karen, Edwards, Robert D., Toon, Alicia, Külheim, Carsten
... Resolving the phylogenetic relationships of closely related species using a small set of loci is challenging as sufficient information may not be captured from a limited sample of the genome. Relying on few loci can also be problematic when conflict between gene-trees arises from incomplete lineage sorting and/or ongoing hybridization, problems especially likely in recently diverged lineages. Here, we developed a method using limited genomic resources that allows identification of many low copy candidate loci from across the nuclear and chloroplast genomes, design probes for target capture and sequence the captured loci. To validate our method we present data from Eucalyptus and Melaleuca, two large and phylogenetically problematic genera within the Myrtaceae family. With one annotated genome, one transcriptome and two whole-genome shotgun sequences of one Eucalyptus and four Melaleuca species, respectively, we identified 212 loci representing 263 kbp for targeted sequence capture and sequencing. Of these, 209 were successfully tested from 47 samples across five related genera of Myrtaceae. The average percentage of reads mapped back to the reference was 57.6% with coverage of more than 20 reads per position across 83.5% of the data. The methods developed here should be applicable across a large range of taxa across all kingdoms. The core methods are very flexible, providing a platform for various genomic resource availabilities and are useful from shallow to deep phylogenies.
Contributors: Bullard, Kristen A., Cox, Stephen, Ferry, Barbara, Lasker, Polly, Zwicker, Sue, Bullard, Kristen, Cox, Stephen, Ferry, Barbara, Lasker, Polly, Zwicker, Sue
Contributors: Gripenberg, Sofia, Basset, Yves, Lewis, Owen T., Terry, J. Christopher D., Wright, S. Joseph, Simón, Indira, Fernández, D. Catalina, Cedeño-Sanchez, Marjorie, Rivera, Marleny, Barrios, Héctor
... The top-down and indirect effects of insects on plant communities depend on patterns of host use, which are often poorly documented, particularly in species-rich tropical forests. At Barro Colorado Island, Panama, we compiled the first food web quantifying trophic interactions between the majority of co-occurring woody plant species and their internally feeding insect seed predators. Our study is based on more than 200 000 fruits representing 478 plant species, associated with 369 insect species. Insect host-specificity was remarkably high: only 20% of seed predator species were associated with more than one plant species, while each tree species experienced seed predation from a median of two insect species. Phylogeny, but not plant traits, explained patterns of seed predator attack. These data suggest that seed predators are unlikely to mediate indirect interactions such as apparent competition between plant species, but are consistent with their proposed contribution to maintaining plant diversity via the Janzen-Connell mechanism.