Climate reconstruction analysis using coexistence likelihood estimation (CRACLE): a method for the estimation of climate using vegetation

A feather hydrogen (δ2H) isoscape for Brazil

Spatial patterns of stable isotopes in animal tissues or “isoscapes” can be used to investigate animal origins in a range of ecological and forensic investigations. Here, we developed a feather hydrogen isotope (δ²H_f) isoscape for Brazil based on 192 samples of feathers from the family Thraupidae from scientific collections. Raw values of δ²H_f ranged from -107.3 to +5.0‰, with higher values at the Caatinga biome (northeast Brazil) and lower values at the Amazon and Pantanal. A Random Forest (RF) method was used to model the spatial surface, using a range of environmental data as auxiliary variables. The RF model indicated a negative relationship between δ²H_f and Mean Annual Precipitation, Precipitation in the Warmest Quarter, and Annual Temperature Range and positive relationships for amount-weighted February-April precipitation δ²H (δ²H_p(Feb-April)) and Mean Annual Solar Radiation. Modelled δ²H_f values ranged from -85.7 to -13.6‰. Ours is the first δ²H_f isoscape for Brazil that can greatly assist our understanding of both ecological and biogeochemical processes controlling spatial variation in δ²H for this region. This isoscape can be used with caution, due to its poor predictive power (as found in other tropical regions) and can benefit from new sample input, new GNIP data, ecological and physiological studies, and keratin standard material better encompassing the range in feather samples from Brazil. So, we encourage new attempts to build more precise feather H isoscapes, as well as isoscapes based on other elements.

Spatial distribution of soil δ13C in the central Brazilian savanna

Stable carbon isotope ratios (δ¹³C) of soil record information regarding C₃ and C₄ plants at the landscape scale that can be used to document vegetation distribution patterns. The Central Brazilian savanna (locally called the Cerrado) has a substantial potential to develop studies of patterns of dynamics and distribution of soil δ¹³C, due to its environmental diversity. The purpose of this work was to develop a spatial model of soil δ¹³C (soil δ¹³C isoscape) to the Cerrado, based on multiple linear regression analysis, and compare the results with the existing model to obtain greater detail of the soil δ¹³C distribution. The model used 219 soil samples (0-20 cm depth) and a set of climatic, pedological, topographic, and vegetation correlations. The soil δ¹³C isoscape model presented amplitude between -29‰ and -13‰, with the highest estimated values in the southern and the lowest values in the northern of the Cerrado. Results indicate that soil δ¹³C, by reflecting the relative contribution of C₃ and C₄ species to plant community productivity, served as a proxy indicator of the vegetation history at the landscape scale for the Central Brazilian savanna. Despite the large sampling effort, there are still regions with some gaps that the model could not estimate. However, the soil δ¹³C isoscape model filled most the existing gaps and provided greater detail of some unique local aspects of the Cerrado.

Neogene precipitation, vegetation, and elevation history of the Central Andean Plateau

Andean uplift played a fundamental role in shaping South American climate and species distribution, but the relationship between the rise of the Andes, plant composition, and local climatic evolution is poorly known. We investigated the fossil record (pollen, leaves, and wood) from the Neogene of the Central Andean Plateau and documented the earliest evidence of a puna-like ecosystem in the Pliocene and a montane ecosystem without modern analogs in the Miocene. In contrast to regional climate model simulations, our climate inferences based on fossil data suggest wetter than modern precipitation conditions during the Pliocene, when the area was near modern elevations, and even wetter conditions during the Miocene, when the cordillera was around ~1700 meters above sea level. Our empirical data highlight the importance of the plant fossil record in studying past, present, and future climates and underscore the dynamic nature of high elevation ecosystems.

Temperate rainforests near the South Pole during peak Cretaceous warmth

The mid-Cretaceous period was one of the warmest intervals of the past 140 million years^1-5, driven by atmospheric carbon dioxide levels of around 1,000 parts per million by volume⁶. In the near absence of proximal geological records from south of the Antarctic Circle, it is disputed whether polar ice could exist under such environmental conditions. Here we use a sedimentary sequence recovered from the West Antarctic shelf-the southernmost Cretaceous record reported so far-and show that a temperate lowland rainforest environment existed at a palaeolatitude of about 82° S during the Turonian-Santonian age (92 to 83 million years ago). This record contains an intact 3-metre-long network of in situ fossil roots embedded in a mudstone matrix containing diverse pollen and spores. A climate model simulation shows that the reconstructed temperate climate at this high latitude requires a combination of both atmospheric carbon dioxide concentrations of 1,120-1,680 parts per million by volume and a vegetated land surface without major Antarctic glaciation, highlighting the important cooling effect exerted by ice albedo under high levels of atmospheric carbon dioxide.

cRacle: R tools for estimating climate from vegetation

PREMISE

The Climate Reconstruction Analysis using Coexistence Likelihood Estimation (CRACLE) method utilizes a robust set of modeling tools for estimating climate and paleoclimate from vegetation using large repositories of biodiversity data and open access R software.

METHODS

Here, we implement a new R package for the estimation of climate from extant and fossil vegetation. The 'cRacle' package implements functions for data access, aggregation, and modeling to estimate climate from plant community compositions. 'cRacle' is modular and includes many best-practice features.

RESULTS

Performance tests using modern vegetation survey data from North and South America shows that CRACLE outperforms alternative methods. CRACLE estimates of mean annual temperature are usually within 1°C of the actual values when optimal model parameters are used. Generalized boosted regression (GBR) model correction improves CRACLE estimates by reducing bias.

DISCUSSION

CRACLE provides accurate estimates of climate based on the composition of modern plant communities. Non-parametric CRACLE modeling coupled with GBR model correction produces the most accurate results to date. The 'cRacle' R package streamlines the estimation of climate from plant community data, which will make this modeling more accessible to a wider range of users.

Ecometabolomic Analysis of Wild Populations of Pilocarpus pennatifolius (Rutaceae) Using Unimodal Analyses

Studies examining the diversity of plant specialized metabolites suggest that biotic and abiotic pressures greatly influence the qualitative and quantitative diversity found in a species. Large geographic distributions expose a species to a great variety of environmental pressures, thus providing an enormous opportunity for expression of environmental plasticity. Pilocarpus, a neotropical genus of Rutaceae, is rich in alkaloids, terpenoids, and coumarins, and is the only commercial source of the alkaloid pilocarpine for the treatment of glaucoma. Overharvesting of species in this genus for pilocarpine, has threatened natural populations of the species. The aim of this research was to understand how adaptation to environmental variation shapes the metabolome in multiple populations of the widespread species Pilocarpus pennatifolius. LCMS data from alkaloid and phenolic extracts of leaf tissue were analyzed with environmental predictors using unimodal unconstrained and constrained ordination methods for an untargeted metabolomics analysis. PLS-DA was used to further confirm the chemoecotypes of each site. The most important variables contributing to the alkaloid variation between the sites: mean temperature of wettest quarter, as well as the soil content of phosphorus, magnesium, and base saturation (V%). The most important contributing to the phenolic variation between the sites: mean temperature of the wettest quarter, temperature seasonality, calcium and soil electrical conductivity. This research will have broad implications in a variety of areas including biocontrol for pests, environmental and ecological plant physiology, and strategies for species conservation maximizing phytochemical diversity.