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Organismal physiology is widely regulated by the molecular circadian clock, a feedback loop composed of protein complexes whose members are enriched in intrinsically disordered regions. These regions can mediate protein-protein interactions via SLiMs, but the contribution of these disordered regions to clock protein interactions had not been elucidated. To determine the functionality of these disordered regions, we applied a synthetic peptide microarray approach to the disordered clock protein FRQ inNeurospora crassa. We identified residues required for FRQ’s interaction with its partner protein FRH, the mutation of which demonstrated FRH is necessary for persistent clock oscillations but not repression of transcriptional activity. Additionally, the microarray demonstrated an enrichment of FRH binding to FRQ peptides with a net positive charge. We found that positively charged residues occurred in significant “blocks” within the amino acid sequence of FRQ and that ablation of one of these blocks affected both core clock timing and physiological clock output. Finally, we found positive charge clusters were a commonly shared molecular feature in repressive circadian clock proteins. Overall, our study suggests a mechanistic purpose for positive charge blocks and yielded insights into repressive arm protein roles in clock function.

 

Intrinsically disordered regions (IDRs) are ubiquitous across all domains of life and play a range of functional roles. While folded domains are generally well described by a stable three-dimensional structure, IDRs exist in a collection of interconverting states known as an ensemble. This structural heterogeneity means that IDRs are largely absent from the Protein Data Bank, contributing to a lack of computational approaches to predict ensemble conformational properties from sequence. Here we combine rational sequence design, large-scale molecular simulations and deep learning to develop ALBATROSS, a deep-learning model for predicting ensemble dimensions of IDRs, including the radius of gyration, end-to-end distance, polymer-scaling exponent and ensemble asphericity, directly from sequences at a proteome-wide scale. ALBATROSS is lightweight, easy to use and accessible as both a locally installable software package and a point-and-click-style interface via Google Colab notebooks. We first demonstrate the applicability of our predictors by examining the generalizability of sequence–ensemble relationships in IDRs. Then, we leverage the high-throughput nature of ALBATROSS to characterize the sequence-specific biophysical behavior of IDRs within and between proteomes.

 

Hyperspectral remote sensing has the potential to map numerous attributes of the Earth’s surface, including spatial patterns of biological diversity. Grasslands are one of the largest biomes on Earth. Accurate mapping of grassland biodiversity relies on spectral discrimination of endmembers of species or plant functional types. We focused on spectral separation of grass lineages that dominate global grassy biomes: Andropogoneae (C₄), Chloridoideae (C₄), and Pooideae (C₃). We examined leaf reflectance spectra (350–2,500 nm) from 43 grass species representing these grass lineages from four representative grassland sites in the Great Plains region of North America. We assessed the utility of leaf reflectance data for classification of grass species into three major lineages and by collection site. Classifications had very high accuracy (94%) that were robust to site differences in species and environment. We also show an information loss using multispectral sensors, that is, classification accuracy of grass lineages using spectral bands provided by current multispectral satellites is much lower (accuracy of 85.2% and 61.3% using Sentinel 2 and Landsat 8 bands, respectively). Our results suggest that hyperspectral data have an exciting potential for mapping grass functional types as informed by phylogeny. Leaf‐level hyperspectral separability of grass lineages is consistent with the potential increase in biodiversity and functional information content from the next generation of satellite‐based spectrometers.

 

Grasslands and savannas exist across a wide range of climates. Mesic savannas, with highly variable tree densities, are particularly misunderstood and understudied in comparison to arid and semi‐arid savannas. North America contains historically extensive mesic savannas dominated by longleaf pine. Longleaf pine savannas may have once been the largest savanna type on North America, yet these ecosystems have been overlooked in global syntheses. Excluding these “Forgotten Ecosystems” from global syntheses biases our understanding of savanna biogeography and distribution.

We assessed the evolutionary history and biogeography of longleaf pine savannas. We then harmonize plot data from longleaf savannas with plot data from valuable existing global synthesis of savannas on other continents. We show that longleaf pine savannas occur in a strikingly distinct climate space compared to savannas on Africa, Australia, and South America, and are unique in having wide ranging tree basal areas.

Grass‐dominated ecosystems are increasingly recognized as being ancient and biologically diverse, yet threatened and undervalued. A new synthesis of savanna ecosystems considering their full range of distributions is needed to understand their ecology and conservation status. Interestingly, the closest analogues to North American savannas and their relatives in Mesoamerica and the Caribbean may be Asian savannas, which also contain mesic fire‐driven pine savannas and have been similarly neglected in existing global syntheses.

 

Plants with the C₄photosynthesis pathway typically respond to climate change differently from more common C₃-type plants, due to their distinct anatomical and biochemical characteristics. These different responses are expected to drive changes in global C₄and C₃vegetation distributions. However, current C₄vegetation distribution models may not predict this response as they do not capture multiple interacting factors and often lack observational constraints. Here, we used global observations of plant photosynthetic pathways, satellite remote sensing, and photosynthetic optimality theory to produce an observation-constrained global map of C₄vegetation. We find that global C₄vegetation coverage decreased from 17.7% to 17.1% of the land surface during 2001 to 2019. This was the net result of a reduction in C₄natural grass cover due to elevated CO₂favoring C₃-type photosynthesis, and an increase in C₄crop cover, mainly from corn (maize) expansion. Using an emergent constraint approach, we estimated that C₄vegetation contributed 19.5% of global photosynthetic carbon assimilation, a value within the range of previous estimates (18–23%) but higher than the ensemble mean of dynamic global vegetation models (14 ± 13%; mean ± one standard deviation). Our study sheds insight on the critical and underappreciated role of C₄plants in the contemporary global carbon cycle.

 

Biogeographic history can set initial conditions for vegetation community assemblages that determine their climate responses at broad extents that land surface models attempt to forecast. Numerous studies have indicated that evolutionarily conserved biochemical, structural, and other functional attributes of plant species are captured in visible-to-short wavelength infrared, 400 to 2,500 nm, reflectance properties of vegetation. Here, we present a remotely sensed phylogenetic clustering and an evolutionary framework to accommodate spectra, distributions, and traits. Spectral properties evolutionarily conserved in plants provide the opportunity to spatially aggregate species into lineages (interpreted as “lineage functional types” or LFT) with improved classification accuracy. In this study, we use Airborne Visible/Infrared Imaging Spectrometer data from the 2013 Hyperspectral Infrared Imager campaign over the southern Sierra Nevada, California flight box, to investigate the potential for incorporating evolutionary thinking into landcover classification. We link the airborne hyperspectral data with vegetation plot data from 1372 surveys and a phylogeny representing 1,572 species. Despite temporal and spatial differences in our training data, we classified plant lineages with moderate reliability (Kappa = 0.76) and overall classification accuracy of 80.9%. We present an assessment of classification error and detail study limitations to facilitate future LFT development. This work demonstrates that lineage-based methods may be a promising way to leverage the new-generation high-resolution and high return-interval hyperspectral data planned for the forthcoming satellite missions with sparsely sampled existing ground-based ecological data.

 

The 17th-century colonization of North America brought thousands of Europeans to Indigenous lands in the Delaware region, which comprises the eastern boundary of the Chesapeake Bay in what is now the Mid- Atlantic region of the United States.1 The demographic features of these initial colonial migrations are not uni- formly characterized, with Europeans and European-Americans migrating to the Delaware area from other countries and neighboring colonies as single persons or in family units of free persons, indentured servants, or tenant farmers.2 European colonizers also instituted a system of racialized slavery through which they forcibly transported thousands of Africans to the Chesapeake region. Historical information about African- descended individuals in the Delaware region is limited, with a population estimate of less than 500 persons by 1700 CE.3,4 To shed light on the population histories of this period, we analyzed low-coverage genomes of 11 individuals from the Avery’s Rest archaeological site (circa 1675–1725 CE), located in Delaware. Previous osteological and mitochondrial DNA (mtDNA) sequence analyses showed a southern group of eight individ- uals of European maternal descent, buried 15–20 feet from a northern group of three individuals of African maternal descent.5 Autosomal results further illuminate genomic similarities to Northwestern European refer- ence populations or West and West-Central African reference populations, respectively. We also identify three generations of maternal kin of European ancestry and a paternal parent-offspring relationship between an adult and child of African ancestry. These findings expand our understanding of the origins and familial relationships in late 17th and early 18th century North America. 

Evolutionary relatedness underlies patterns of functional diversity in the natural world. Hyperspectral remote sensing has the potential to detect these patterns in plants through inherited patterns of leaf reflectance spectra. We collected leaf reflectance data across the California flora from plants grown in a common garden. Regions of the reflectance spectra vary in the depth and strength of phylogenetic signal. We also show that these differences are much greater than variation due to the geographic origin of the plant. At the phylogenetic extent of the California flora, spectral variation explained by the combination of ecotypic variation (divergent evolution) and convergent evolution of disparate lineages was minimal (3%–7%) but statistically significant. Interestingly, at the extent of a single genus (Arctostaphylos) no unique variation could be attributed to geographic origin. However, up to 18% of the spectral variation amongArctostaphylosindividuals was shared between phylogeny and intraspecific variation stemming from ecotypic differences (i.e., geographic origin). Future studies could conduct more structured experiments (e.g., transplants or observations along environmental gradients) to disentangle these sources of variation and include other intraspecific variation (e.g., plasticity). We constrain broad‐scale spectral variability due to ecotypic sources, providing further support for the idea that phylogenetic clusters of species might be detectable through remote sensing. Phylogenetic clusters could represent a valuable dimension of biodiversity monitoring and detection.

 

Both historically and in terms of practiced academic organization, the anticipation should be that a flourishing synergistic interface exists between statistics and operations research in general, and between spatial statistics/econometrics and spatial optimization in particular. Unfortunately, for the most part, this expectation is false. The purpose of this paper is to address this existential missing link by focusing on the beneficial contributions of spatial statistics to spatial optimization, via spatial autocorrelation (i.e., dis/similar attribute values tend to cluster together on a map), in order to encourage considerably more future collaboration and interaction between contributors to their two parent bodies of knowledge. The key basic statistical concept in this pursuit is the median in its bivariate form, with special reference to the global and to sets of regional spatial medians. One-dimensional examples illustrate situations that the narrative then extends to two-dimensional illustrations, which, in turn, connects these treatments to the spatial statistics centrography theme. Because of computational time constraints (reported results include some for timing experiments), the summarized analysis restricts attention to problems involving one global and two or three regional spatial medians. The fundamental and foundational spatial, statistical, conceptual tool employed here is spatial autocorrelation: geographically informed sampling designs—which acknowledge a non-random mixture of geographic demand weight values that manifests itself as local, homogeneous, spatial clusters of these values—can help spatial optimization techniques determine the spatial optima, at least for location-allocation problems. A valuable discovery by this study is that existing but ignored spatial autocorrelation latent in georeferenced demand point weights undermines spatial optimization algorithms. All in all, this paper should help initiate a dissipation of the existing isolation between statistics and operations research, hopefully inspiring substantially more collaborative work by their professionals in the future.