Joseph Craine

Jonah Ventures, LLC

As freshwater algae respond strongly to environmental conditions, algal communities are routinely used as indicators of aquatic health. Algal bioassessments have historically relied upon microscopy‐based identifications that are typically slow, expensive, taxonomically restricted, and inconsistent across analysts and time. Metabarcoding of water co...

Australia’s distinctive biogeography means that it is sometimes considered an ecologically unique continent with biological and abiotic features that are not comparable to those observed in the rest of the world. This leaves some researchers unclear as to whether findings from Australia apply to systems elsewhere (or vice-versa), which has conseque...

Here we provide the ‘Global Spectrum of Plant Form and Function Dataset’, containing species mean values for six vascular plant traits. Together, these traits –plant height, stem specific density, leaf area, leaf mass per area, leaf nitrogen content per dry mass, and diaspore (seed or spore) mass – define the primary axes of variation in plant form...

The productivity of ecosystems and their capacity to support life depends on access to reactive nitrogen (N). Over the past century, humans have more than doubled the global supply of reactive N through industrial and agricultural activities. However, long-term records demonstrate that N availability is declining in many regions of the world. React...

The Great Salt Lake (GSL) is a unique hypersaline system with an understudied phytoplankton assemblage supporting a productive open water ecosystem in the largest embayment of the lake, Gilbert Bay. Determination of phytoplankton by microscopy has practical limitations that can constrain the scope of a study, but DNA metabarcoding may improve upon...

The rivers of Appalachia (United States) are among the most biologically diverse freshwater ecosystems in the temperate zone and are home to numerous endemic aquatic organisms. Throughout the Central Appalachian ecoregion, extensive surface coal mines generate alkaline mine drainage that raises the pH, salinity, and trace element concentrations in...

North American plains bison ( Bison bison ) have been reintroduced across their former range, yet we know too little about their current diet to understand what drove their past migrations as well as observed continental-scale variation in weight gain and reproduction. In order to better understand the seasonal diets of bison at the continental sca...

Motivation Trait data are fundamental to the quantitative description of plant form and function. Although root traits capture key dimensions related to plant responses to changing environmental conditions and effects on ecosystem processes, they have rarely been included in large‐scale comparative studies and global models. For instance, root trai...

This paper introduces a modular processing chain to derive global high-resolution maps of leaf traits. In particular, we present global maps at 500 m resolution of specific leaf area, leaf dry matter content, leaf nitrogen and phosphorus content per dry mass, and leaf nitrogen/phosphorus ratio. The processing chain exploits machine learning techniq...

The trajectory of nitrogen availability in terrestrial ecosystems over the past century is still poorly understood due to a lack of monitoring and proxy‐based reconstructions. For the Northern Great Plains, Brookshire et al. (citation) analyze satellite‐based reconstructions of greenness and foliar nutrition and isotopic composition from herbarium...

Motivation Trait data are fundamental to quantitatively describe plant form and function. Although root traits capture key dimensions related to plant responses to changing environmental conditions and effects on ecosystem processes, they have rarely been included in large-scale comparative studies and global models. For instance, root traits remai...

The majority of variation in six traits critical to the growth, survival and reproduction of plant species is thought to be organised along just two dimensions, corresponding to strategies of plant size and resource acquisition. However, it is unknown whether global plant trait relationships extend to climatic extremes, and if these interspecific r...

Background Nutrition is a key determinant of North American plains bison (Bison bison) weight gain and reproduction, yet little is known about what bison eat and the pattern of nutritional stress across their distribution. Aims In order to better understand patterns of bison nutrition across broad climatic gradients, bison fecal material was sampl...

Aim Plant trait databases often contain traits that are correlated, but for whom direct (undirected statistical dependency) and indirect (mediated by other traits) connections may be confounded. The confounding of correlation and connection hinders our understanding of plant strategies, and how these vary among growth forms and climate zones. We id...

Large herbivores that survived the Pleistocene/Holocene transition are hypothesized to have been forced to take refuge, as a result of environmental changes and human pressure, into forest habitats. Today, there is an open question of the degree to which extant large herbivores are well adapted to the forests that allowed for the herbivores’ persis...

Questions What is the functional trait variation of European temperate grasslands and how does this reflect global patterns of plant form and function? Do habitat specialists show trait differentiation across habitat types? Location Europe. Methods We compiled 18 regeneration and non‐regeneration traits for a continental species pool consisting o...

Grass leaf shape is a strong indicator of their habitat with linear leaves predominating in open areas and ovate leaves distinguishing forest‐associated grasses. This pattern among extant species suggests that ancestral shifts between forest and open habitats may have coincided with changes in leaf shape or size. We tested relationships between hab...

Human societies depend on an Earth system that operates within a constrained range of nutrient availability, yet the recent trajectory of terrestrial nitrogen (N) availability is uncertain. Examining patterns of foliar N concentrations and isotope ratios (δ15N) from more than 43,000 samples acquired over 37 years, here we show that foliar N concent...

A substantial body of evidence has demonstrated that biodiversity stabilizes ecosystem functioning over time in grassland ecosystems. However, the relative importance of different facets of biodiversity underlying the diversity-stability relationship remains unclear. Here we use data from 39 grassland biodiversity experiments and structural equatio...

Diets during critical brooding and winter periods likely influence the growth of Lesser Prairie-Chicken (Tympanuchus pallidicinctus) populations. During the brooding period, rapidly growing Lesser Prairie-Chicken chicks have high calorie demands and are restricted to foods within immediate surroundings. For adults and juveniles during cold winters,...

The environmental health of aquatic ecosystems is critical to society, yet traditional assessments of water quality have limited utility for some bodies of water such as large rivers. Sequencing of environmental DNA (eDNA) has the potential to complement if not replace traditional sampling of biotic assemblages for the purposes of reconstructing aq...

The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from...

Alignment of rbcL, ndhF, matK, and trnK intron, excluding gapped sites and including positively selected sites, for 250 grass accessions (Dataset B); PHYLIP format.

Alignment of plastome coding regions, excluding gapped sites and positively selected sites, for 250 grass accessions (Dataset H); PHYLIP format.

Bootstrap support ≥50% for shared clades across all trees. Clades were first named based on tree X, a reference tree. Unique clades in non-reference trees were also named and scored across all trees.

Values for dN, dS and omega for each CDS with a test for positive or purifying selection using the codon-based Z test of selection on default parameters.

Alignment of rbcL, ndhF, matK, and trnK intron excluding gapped sites and positively selected sites, for 250 grass accessions (Dataset D); PHYLIP format.

Alignment of plastome coding regions, including gapped sites and positively selected sites, for 250 grass accessions (Dataset E); PHYLIP format.

Alignment of complete plastomes, including gapped sites and positively selected sites, for 250 grass accessions (Dataset W); PHYLIP format.

Maximum likelihood (ML) phylograms of 250 grasses based on 14 partitions of the plastome. Letters identifying each of the 14 trees correspond to the data partitions as identified in Table 2. (A) rbcL, ndhF, matK, and trnK intron, including gapped sites and positively selected sites. (B) rbcL, ndhF, matK, and trnK intron, excluding gapped sites and...

Alignment of plastome coding regions, including gapped sites and excluding positively selected sites, for 250 grass accessions (Dataset G); PHYLIP format.

Alignment of plastome noncoding regions, excluding gapped sites, for 250 grass accessions (Dataset R); PHYLIP format.

Alignment of complete plastomes, excluding gapped sites and including positively selected sites, for 250 grass accessions (Dataset X); PHYLIP format.

Alignment of complete plastomes, including gapped sites and excluding positively selected sites, for 250 grass accessions (Dataset Y); PHYLIP format.

Alignment of complete plastomes, excluding gapped sites and positively selected sites, for 250 grass accessions (Dataset Z); PHYLIP format.

Information on previously published and new plastomes, including GenBank accession numbers, source publications, and classification details following Soreng et al. (2017). Accession numbers in bold identify plastomes newly generated as part of this study.

Alignment of rbcL, ndhF, matK, and trnK intron sequences, including gapped sites and positively selected sites, for 250 grass accessions (Dataset A); PHYLIP format.

Alignment of rbcL, ndhF, matK, and trnK intron, including gapped sites and excluding positively selected sites, for 250 grass accessions (Dataset C); PHYLIP format.

Alignment of plastome coding regions, excluding gapped sites and including positively selected sites, for 250 grass accessions (Dataset F); PHYLIP format.

Alignment of plastome noncoding regions, including gapped sites, for 250 grass accessions (Dataset Q); PHYLIP format.

Background and aims Although a number of different factors influence C and N isotopic fractionation of organic matter, the δ¹³C and δ¹⁵N values of soil organic matter both tend to increase with soil depth, following similar trajectories. This similarity has not been investigated at the global scale. As microbial decomposition increases organic matt...

Leaf Economics Spectrum (LES) trait variation underpins multiple agroecological processes and many prominent crop yield models. While there are numerous independent studies assessing trait variation in crops, to date there have been no comprehensive assessments of intraspecific trait variation (ITV) in LES traits for wheat and maize: the world’s mo...

Variation across climate gradients in the isotopic composition of nitrogen (N) and carbon (C) in foliar tissues has the potential to reveal ecological processes related to N and water availability. However, it has been a challenge to separate spatial patterns related to direct effects of climate from effects that manifest indirectly through species...

Forests cover 30% of the terrestrial Earth surface and are a major component of the global carbon (C) cycle. Humans have doubled the amount of global reactive nitrogen (N), increasing deposition of N onto forests worldwide. However, other global changes—especially climate change and elevated atmospheric carbon dioxide concentrations—are increasing...

Significance Currently, Earth system models (ESMs) represent variation in plant life through the presence of a small set of plant functional types (PFTs), each of which accounts for hundreds or thousands of species across thousands of vegetated grid cells on land. By expanding plant traits from a single mean value per PFT to a full distribution per...

The study of the microbial communities has gained traction in recent years with the advent of next-generation sequencing with, or without, PCR-based amplification of the 16S ribosomal RNA region. Such studies have been applied to topics as diverse as human health and environmental ecology. Fewer studies have investigated taxa outside of bacteria, h...

Archaea, diatom and fungus PCA analyses. PCA analysis of archaea, diatom and fungal datasets reveal that the four sample groups produce distinct sample groups. PC1 vs PC2 and PC2 vs PC3 are presented for both datasets. (TIFF)

18S rRNA diatom dataset OTU loadings and taxa. (XLSX)

OTU loadings and taxa for analysis of all OTUs from each dataset combined. (XLSX)

Sequencing read numbers. (XLSX)

16S rRNA archaea dataset OTU loadings and taxa. (XLSX)

16S rRNA bacteria dataset OTU loadings and taxa. (XLSX)

23S rRNA algae dataset OTU loadings and taxa. (XLSX)

ITS fungus dataset OTU loadings and taxa. (XLSX)

Freshwater aquatic ecosystems provide a wide range of ecosystem services, yet provision of these services is increasingly threatened by human activities. Directly quantifying freshwater biotic assemblages has long been a proxy for assessing changing environmental conditions, yet traditional aquatic biodiversity assessments are often time consuming,...

With over 1 billion cattle in the world as well as over 2 billion sheep, goats and buffalo, these animals contribute approximately 15% of the global human protein supply while producing a significant proportion of anthropogenic emissions of greenhouse gases and global nutrient fluxes. Despite increasing reliance on grazers for protein production gl...

Ecologists traditionally use environmental parameters to predict successional shifts in compositional characteristics of local species assemblages (environmental control). Another important focus in ecology is to understand functional roles of species assemblages in determining local environmental properties (diversity control). Then, the question...

Despite the prevalence and costs of allergic diseases caused by pollen, we know little about the distributions of allergenic and non-allergenic pollen inside and outside homes at the continental scale. To better understand patterns in potential pollen diversity across the United States, we used DNA sequencing of a chloroplast marker gene to identif...

Ecosystem functioning relies heavily on below‐ground processes, which are largely regulated by plant fine‐roots and their functional traits. However, our knowledge of fine‐root trait distribution relies to date on local‐ and regional‐scale studies with limited numbers of species, growth forms and environmental variation. We compiled a world‐wide fi...

How climate and rising carbon dioxide concentrations (pCO2) have influenced competition between C3 and C4 plants over the last 50 years is a critical uncertainty in climate change research. Here we used carbon isotope (δ13C) values of the saprotrophic lawn fungus Amanita thiersii to integrate the signal of C3 and C4 carbon in samples collected betw...

There is wide agreement that anthropogenic climate warming has influenced the phenology of forests during the late twentieth and early twenty-first centuries1,2. Longer growing seasons can lead to increased photosynthesis and productivity3, which would represent a negative feedback to rising CO2 and consequently warming4,5. Alternatively, increased...

Environmental conditions experienced during early growth and development markedly shape phenotypic traits. Consequently, individuals of the same cohort may show similar life-history tactics throughout life. Conditions experienced later in life, however, could fine-tune these initial differences, either increasing (cumulative effect) or decreasing (...

In North America, it has been shown that cattle in warmer, drier grasslands have lower quality diets than those cattle grazing cooler, wetter grasslands, which suggests warming will increase nutritional stress and reduce weight gain. Yet, little is known about how the plant species that comprise cattle diets change across these gradients and whethe...

Background: Panicoideae are the second largest subfamily in Poaceae (grass family), with 212 genera and approximately 3316 species. Previous studies have begun to reveal relationships within the subfamily, but largely lack resolution and/or robust support for certain tribal and subtribal groups. This study aims to resolve these relationships, as w...

Significance This research breaks new ground by showing that, contrary to generally accepted theories of ecosystem development, calcium depletion has been occurring for millennia as a natural consequence of long-term ecosystem development. This natural process predisposed forest ecosystems in the region to detrimental responses to acid rain in the...

Frequent burning is a crucial ecological and economic component of the Kansas Flint Hills. Although burning is important for the preservation of tallgrass prairie and improving livestock production, it has become a controver- sial societal issue because of its potential impact on air quality standards. Over the past 80 years, recommenda- tions on b...

Plant functional traits are the features (morphological, physiological, phenological) that represent ecological strategies and determine how plants respond to environmental factors, affect other trophic levels and influence ecosystem properties. Variation in plant functional traits, and trait syndromes, has proven useful for tackling many important...