CRACLE validates long hypothesized interactions between climate and local associations of plant species. Furthermore, CRACLE successfully estimates climate that is consistent with the widely used WorldClim model and therefore may be applied to the quantitative estimation of paleoclimate in future studies.

The Late Quaternary packrat (Neotoma spp.) midden plant macrofossil record in western North America is an exceptional record of biotic change that provides strong evidence of past climate. In this study, we generate quantitative estimates of climate from plant community composition of more than 600 individual paleomiddens over the past 50,000 years. Here we present the first large-scale application of CRACLE (Climate Reconstruction Analysis using Coexistence Likelihood Estimation), a quantitative climate inference method that uses plant community composition as a climate proxy under the individualistic concept of plant community assembly. The results are spatiotemporally specific estimates of temperature, precipitation, available moisture, and seasonal patterns that are consistent with well understood global climate patterns but provide previously unavailable detail and precision of the regional paleoclimate in western North America. Rapid warming is estimated at the Pleistocene-Holocene transition, at a conservative estimate of ca. 1°C per millennium. Previously projected future temperature increases suggest a rate of increase of more than 2°C over the next century, an astonishing 10× the rate experienced at any point during the past 50,000 years in Western North America. These analyses form a baseline demonstration of how the growing paleoecological record of packrat midden plant macrofossils can provide quantitative estimates of paleoclimate that aid in understanding the complexities of, and biotic responses to the regional climate system. This work is the first synthetic application of any paleoclimate estimation method to packrat midden plant macrofossils.

Premise of the Study DNA may be preserved for thousands of years in very cold or dry environments, and plant tissue fragments and pollen trapped in soils and shallow aquatic sediments are well suited for the molecular characterization of past floras. However, one obstacle in this area of study is the limiting bias in the bioinformatic classification of short fragments of degraded DNA from the large, complex genomes of plants.MethodsTo establish one possible baseline protocol for the rapid classification of short‐read shotgun metagenomic data for reconstructing plant communities, the read classification programs Kraken, Centrifuge, and MegaBLAST were tested on simulated and ancient data with classification against a reference database targeting plants.ResultsPerformance tests on simulated data suggest that Kraken and Centrifuge outperform MegaBLAST. Kraken tends to be the most conservative approach with high precision, whereas Centrifuge has higher sensitivity. Reanalysis of 13,000 years of ancient sedimentary DNA from North America characterizes potential post‐glacial vegetation succession.DiscussionClassification method choice has an impact on performance and any downstream interpretation of results. The reanalysis of ancient DNA from glacial lake sediments yielded vegetation histories that varied depending on method, potentially changing paleoecological conclusions drawn from molecular evidence.

Plant cell shape is determined by the orientation of cellulose microfibrils in the primary cell wall. Consequently, mutations that affect genes encoding the enzymes responsible for the synthesis of cellulose, namely, the cellulose synthase catalytic subunits, can alter cell shape substantially, particularly in the roots of affected plants. The multiple response expansion1 (mre1) mutant of Arabidopsis thaliana results from a point mutation in the AtCESA3 gene, which encodes one of the three isoforms of the cellulose synthase catalytic subunit required for synthesis of cellulose in the primary cell wall. Phenotypic comparison of the mre1 mutant with three other alleles (ectopic lignification1-1, ectopic lignification1-2 and constitutive expression of vsp1) showed that these four alleles form an allelic series with respect to their root phenotypes, with mre1 being the weakest allele identified to date. These analyses demonstrated that sucrose affects a significant alteration of cell shape in the roots of these mutants and likely suppresses root cell division in them as well, and that the chemical aminoisobutyric acid can suppress these effects of sucrose. Interestingly, the cell walls in the roots of these four AtCESA3 alleles contain different percentages of cellulose, and these percentages correlate with the lengths of the roots and cortex cells in these roots when grown on media containing high levels of sucrose.