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opencc-zeroDec 2015View details →

Data from: Cross-validation strategies for data with temporal, spatial, hierarchical, or phylogenetic structure

Ecological data often show temporal, spatial, hierarchical (random effects), or phylogenetic structure. Modern statistical approaches are increasingly accounting for such dependencies. However, when performing cross-validation, these structures are regularly ignored, resulting in serious underestimation of predictive error. One cause for the poor performance of uncorrected (random) cross-validation, noted often by modellers, are dependence structures in the data that persist as dependence structures in model residuals, violating the assumption of independence. Even more concerning, because often overlooked, is that structured data also provides ample opportunity for overfitting with non-causal predictors. This problem can persist even if remedies such as autoregressive models, generalized least squares, or mixed models are used. Block cross-validation, where data are split strategically rather than randomly, can address these issues. However, the blocking strategy must be carefully considered. Blocking in space, time, random effects or phylogenetic distance, while accounting for dependencies in the data, may also unwittingly induce extrapolations by restricting the ranges or combinations of predictor variables available for model training, thus overestimating interpolation errors. On the other hand, deliberate blocking in predictor space may also improve error estimates when extrapolation is the modelling goal. Here, we review the ecological literature on non-random and blocked cross-validation approaches. We also provide a series of simulations and case studies, in which we show that, for all instances tested, block cross-validation is nearly universally more appropriate than random cross-validation if the goal is predicting to new data or predictor space, or for selecting causal predictors. We recommend that block cross-validation be used wherever dependence structures exist in a dataset, even if no correlation structure is visible in the fitted model residuals, or if the fitted models account for such correlations.

Data from: Local extinctions of obligate frugivores and patch size reduction disrupt the structure of seed dispersal networks

A central problem in ecology is to understand how human impacts affect plant-animal interactions that lead to effective seed dispersal services for plant communities. Seed dispersal services are the outcome of plant-frugivore interactions that often form local networks of interacting species. Recent work has shown that some frugivorous bird species are more critical to network organization than others. Here, we explore how patch size and the potential local extinctions of obligate frugivorous birds affect the reorganization of seed dispersal networks. We examined the structure of 20 empirical seed dispersal networks documented across tropical avian assemblages occupying widely variable habitat patch sizes, a surrogate of the amount of remaining habitat. Networks within small forest patches consistently supported both lower plant and bird species richness. Forest patch size was positively associated with nestedness, indicating that reductions in patch size disrupted the nested organization of seed dispersal networks. Obligate frugivores, especially large-bodied species, were almost entirely absent from small forest patches. Analysis at the species level showed that obligate frugivores formed the core of interacting species, connecting species within a given seed dispersal network. Our combined results revealed that patch size reduction erodes frugivorous bird diversity, thereby affecting the integrity of seed dispersal networks. We highlight the importance of conserving large forest patches to maintain tropical forest functionality.

opencc-zeroDec 2010View details →

Data from: Inferring the origin of populations introduced from a genetically structured native range by approximate Bayesian computation: case study of the invasive ladybird Harmonia axyridis

Correct identification of the source population of an invasive species is a prerequisite for testing hypotheses concerning the factors responsible for biological invasions. The native area of invasive species may be large, poorly known and/or genetically structured. Because the actual source population may not have been sampled, studies based on molecular markers may generate incorrect conclusions about the origin of introduced populations. In this study, we characterized the genetic structure of the invasive ladybird Harmonia axyridis in its native area using various population genetic statistics and methods. We found that H. axyridis native area most likely consisted of two geographically distinct genetic clusters located in eastern and western Asia. We then performed approximate Bayesian computation (ABC) analyses on controlled simulated microsatellite data sets to evaluate: (i) the risk of selecting incorrect introduction scenarios, including admixture between sources, when the populations of the native area are genetically structured and sampling is incomplete, (ii) the ability of ABC analysis to minimize such risks by explicitly including unsampled populations in the scenarios compared. Finally, we performed additional ABC analyses on real microsatellite data sets to retrace the origin of biocontrol and invasive populations of H. axyridis, taking into account the possibility that the structured native area may have been incompletely sampled. We found that the invasive population in eastern North America, which has served as the bridgehead for worldwide invasion by H. axyridis, was probably formed by an admixture between the eastern and western native clusters. This admixture may have facilitated adaptation of the bridgehead population.

opencc-zeroDec 2018View details →

Data from: Genetic variation and structure of Diaphorina citri (Hemiptera:Liviidae) in populations from México

The Asian citrus psyllid, Diaphorina citri Kuwayama, is native to Asia but has recently invaded North America. Asian citrus psyllid is a significant pest of citrus crops by its direct feeding but, more importantly, as the vector of the bacterium 'Candidatus Liberibacter asiaticus', which causes Huanglongbing disease. Asian citrus psyllid was first found in México in 2001 and 2002 and, since then, has spread quickly across the country, suggesting rapid adaptation to new environments. Yet, we lack information on the genetic variation and structure that could facilitate or inhibit adaptation. Using six microsatellite markers, we analyzed genetic variation and structure among six localities in México: three in western states near the Pacific coast and two in the Yucatán Peninsula near the Gulf of México. We found low genetic diversity (no more than three alleles per locus) and intermediate differentiation between all populations. Asian citrus psyllid populations clustered into two genetic groups, but, surprisingly, these clusters were present in western populations. The first group included El Arenal, and the second group included Autlán de Navarro, Colima, and Tecomán. Interestingly, both of the Yucatán populations shared variation from the two clusters, suggesting admixture. We infer that reproductive isolation, barriers to gene flow, local selection, and the possibility of multiple invasions have influenced the current genetic structure of Asian citrus psyllid in México.

Data from: Energetics and electronic structures of perylene confined in carbon nanotubes

The energetics and geometries of perylene encapsulated in carbon nanotubes (CNTs) have been investigated employing density functional theory using the generalized gradient approximation combined with the van der Waals correction. Our calculations show that the encapsulated perylene molecules possess two metastable molecular conformations with respect to the CNT wall, which are almost degenerate with each other. A standing conformation, with respect to the CNT wall, is the ground state conformation for a semiconducting (19,0)CNT, while a lying conformation is the ground state for a metallic (11,11)CNT. Cooperation and competition between perylene-perylene and perylene-CNT interactions cause these possible perylene conformations inside CNTs. However, the electronic structure of the CNT encapsulating the perylene molecules is found to be insensitive to the molecular conformation.

Data from: Calculating structural complexity in phylogenies using ancestral ontologies

Complexity is an important aspect of evolutionary biology, but there are many reasonable concepts of complexity, and its objective measurement is an elusive matter. Here we develop a simple measure of complexity based on counts of elements, incorporating the hierarchical information as represented in anatomical ontologies. Neomorphic and transformational characters are used to identify novelties and individuated morphological regions, respectively. By linking the characters to terms in an anatomical ontology a node-driven approach is implemented, where a node ontology and a complexity score are inferred from the optimization of individual characters on each ancestral or terminal node. From the atomized vector of character scorings, the anatomical ontology is used to integrate the hierarchical structure of morphology in terminals and ancestors. These node ontologies are used to calculate a measure of complexity that can be traced on phylogenetic trees and is harmonious with usual phylogenetic operations. This strategy is compared with a terminal-driven approach, where the complexity scores are calculated only for terminals, and optimized as a continuous character on the internal nodes. These ideas are applied to a real dataset of 166 araneomorph spider species scored for 393 characters, using the Spider Ontology (SPD); complexity scores and transitions are calculated for each node and branch, respectively. This result in a distribution of transitions skewed towards simplification; the transitions in complexity have no apparent correlation with character branch lengths. The node-driven and terminal-driven estimations are generally correlated in the complexity scores, but have higher divergence in the transition values. The structure of the ontology is used to provide complexity scores for organ systems and body parts of the focal groups.

opencc-zeroDec 2011View details →

Data from: Environmental conditions affect spatial genetic structures and dispersal patterns in a solitary rodent

The study of the spatial distribution of relatives in a population under contrasted environmental conditions provides critical insights into the flexibility of dispersal behaviour and the role of environmental conditions in shaping population relatedness and social structure. Yet few studies have evaluated the effects of fluctuating environmental conditions on relatedness structure of solitary species in the wild. The aim of this study was to determine the impact of interannual variations in environmental conditions on the spatial distribution of relatives [spatial genetic structure (SGS)] and dispersal patterns of a wild population of eastern chipmunks (Tamias striatus), a solitary rodent of North America. Eastern chipmunks depend on the seed of masting trees for reproduction and survival. Here, we combined the analysis of the SGS of adults with direct estimates of juvenile dispersal distance during six contrasted years with different dispersal seasons, population sizes and seed production. We found that environmental conditions influences the dispersal distances of juveniles and that male juveniles dispersed farther than females. The extent of the SGS of adult females varied between years and matched the variation in environmental conditions. In contrast, the SGS of males did not vary between years. We also found a difference in SGS between males and females that was consistent with male-biased dispersal. This study suggests that both the dispersal behaviour and the relatedness structure in a population of a solitary species can be relatively labile and change according to environmental conditions.

Data from: Temporal genetic structure in a poecilogonous polychaete: the interplay of developmental mode and environmental stochasticity

Background: Temporal variation in the genetic structure of populations can be caused by multiple factors, including natural selection, stochastic environmental variation, migration, or genetic drift. In benthic marine species, the developmental mode of larvae may indicate a possibility for temporal genetic variation: species with dispersive planktonic larvae are expected to be more likely to show temporal genetic variation than species with benthic or brooded non-dispersive larvae, due to differences in larval mortality and dispersal ability. We examined temporal genetic structure in populations of Pygospio elegans, a poecilogonous polychaete with within-species variation in developmental mode. P. elegans produces either planktonic, benthic, or intermediate larvae, varying both among and within populations, providing a within-species test of the generality of a relationship between temporal genetic variation and larval developmental mode. Results: In contrast to our expectations, our microsatellite analyses of P. elegans revealed temporal genetic stability in the UK population with planktonic larvae, whereas there was variation indicative of drift in temporal samples of the populations from the Baltic Sea, which have predominantly benthic and intermediate larvae. We also detected temporal variation in relatedness within these populations. A large temporal shift in genetic structure was detected in a population from the Netherlands, having multiple developmental modes. This shift could have been caused by local extiction due to extreme environmental conditions and (re)colonization by planktonic larvae from neighboring populations. Conclusions: In our study of P. elegans, temporal genetic variation appears to be due to not only larval developmental mode, but also the stochastic environment of adults. Large temporal genetic shifts may be more likely in marine intertidal habitats (e.g. North Sea and Wadden Sea) which are more prone to environmental stochasticity than the sub-tidal Baltic habitats. Sub-tidal and/or brackish (less saline) habitats may support smaller P. elegans populations and these may be more susceptible to the effects of random genetic drift. Moreover, higher frequencies of asexual reproduction and the benthic larval developmental mode in these populations leads to higher relatedness and contributes to drift. Our results indicate that a general relationship between larval developmental mode and temporal genetic variation may not exist.

opencc-zeroDec 2016View details →

Data from: Protein structure determination using metagenome sequence data

Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families and that metagenome sequence data more than triple the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact-based structure matching, and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the Protein Data Bank. This approach provides the representative models for large protein families originally envisioned as the goal of the Protein Structure Initiative at a fraction of the cost.

Data from: Drone‐based structure‐from‐motion photogrammetry captures grassland sward height variability

Grasslands deliver a range of ecosystem services, including the provision of food and biodiversity, and regulation of soil carbon storage and hydrology. Monitoring schemes are needed to quantify spatial changes in these multiple functions alongside ecosystem degradation. Sward height is widely recognised as a key spatial variable in the provision of these services. Current manual monitoring approaches are labour intensive, and often fail to capture spatial patterns of important features, including sward height. Proximal sensing from small aerial drones carrying lightweight cameras can be transformed into surface height models using image‐based structure‐from‐motion and Multi‐View Stereo‐based approaches; this presents a new opportunity for monitoring the spatial structure of grassland sward height. We combined aerial photographs with field survey data and an open‐source image‐based modelling‐processing workflow to generate sward height measurements for a field comprising mainly Lolium perenne (perennial ryegrass) and Trifolium pratense (red clover). We compared the derived measurements with in situ data captured on the same day using traditional agronomic sward height techniques to determine the quality of the drone‐derived surface model product for sward characterisation. The SfM and Multi‐View Stereo‐based surface model had a mean absolute sward height measurement error of between 3.7 and 4.2 cm. To produce field observations with equivalent quality would require up to 550 sward height measurements for the study site (area: 8,059 m2), which is not feasible over larger extents required for conservation of key species or agronomic purposes. Synthesis and applications. We demonstrate how the collection of precise and detailed information on the spatial structure of grasslands can be made over management‐relevant extents. Aerial digital photographs can be transformed into surface models using an image‐based modelling approach: structure‐from‐motion and Multi‐View Stereo techniques. Image‐based measurements of sward heights were compared with manual sward height data captured on the same day. This novel source of vegetation spatial information could improve sward management for conservation and agronomy applications. The approach supports frequent surveys, at user‐controlled revisit times, and delivers data for spatial monitoring of key grassland functions and services.

Data from: Nuclear and mitochondrial patterns of population structure in North Pacific false killer whales (Pseudorca crassidens)

False killer whales (Pseudorca crassidens) are large Delphinids typically found in deep water far offshore. However, in the Hawaiian Archipelago there are two resident island-associated populations of false killer whales, one in the waters around the main Hawaiian Islands (MHI) and one in the waters around the Northwestern Hawaiian Islands (NWHI). We use mitochondrial DNA (mtDNA) control region sequences and genotypes from 16 nuclear (nucDNA) microsatellite loci from 206 individuals to examine levels of differentiation among the two island-associated populations and offshore animals from the central and eastern North Pacific. Both mtDNA and nucDNA exhibit highly significant differentiation between populations, confirming limited gene flow in both sexes. The mtDNA haplotypes exhibit a strong pattern of phylogeographic concordance, with island-associated populations sharing three closely related haplotypes not found elsewhere in the Pacific. However, nucDNA data suggests that NWHI animals are at least as differentiated from MHI animals as they are from offshore animals. The patterns of differentiation revealed by the two marker types suggest that the island-associated false killer whale populations likely share a common colonization history, but have limited contemporary gene flow.

opencc-zeroJul 2019View details →

Data from: Catalytic self-folding of 2D structures through cascading magnet reactions

While thousands of proteins involved in development of the human body are capable of self-assembling in a distributed manner from merely 20 types of amino acid, macroscopic products that can be assembled spontaneously from `alive' components remains an aspiration in engineering. To attain such a mechanism, a major challenge lies in understanding which attributes from the bio-molecular realm must be leveraged at the macro-scale. Inspired by protein folding, we present a centimetre-size 1D tile chain whose self-folding processes are directed by structure-embedded magnetic interactions, which can theoretically self-assemble into convex 2D structures of any size or shape without the aid of a global `controller'. Each tile holds two magnets contained in paths designed to control their interactions. Once initiated by a magnetic unit (termed Catalyst), the chain self-reconfigures by consuming magnetic potential energy stored between magnet pairs, until the final 2D structure is reached at an energetic minimum. Both simulation and experimental results are presented to illustrate the method's efficacy on chains of arbitrary length. Results demonstrate the promise of a physically implemented, bottom-up, and scalable self-assembly method for novel 2D structure manufacturing, bridging the bio-molecular and mechanical realms.

opencc-zeroSep 2021View details →

Data From: Genetic structure of recently fragmented suburban populations of European stag beetle

Habitat loss and fragmentation due to urbanisation can negatively affect metapopulation persistence when gene flow among populations is reduced and population sizes decrease. Inference of patterns and processes of population connectivity derived from spatial genetic analysis has proven invaluable for conservation and management. However, a more complete account of population dynamics may be obtained by combining spatial and temporal sampling. We, therefore, performed a genetic study on European stag beetle (Lucanus cervus L.) populations in a suburban context using samples collected in three locations and during the period 2002-2016. The sampling area has seen recent landscape changes which resulted in population declines. Through the use of a suite of FST, clustering analysis, individual assignment, and relatedness analysis we assessed fine scale spatiotemporal genetic variation within and among habitat patches using 283 individuals successfully genotyped at 17 microsatellites. Our findings suggested the three locations to hold demographically independent populations, at least over time scales of relevance to conservation, though with higher levels of gene flow in the past. Contrary to expectation from tagging studies, dispersal appeared to be mainly female-biased. Although the life cycle of stag beetle suggests its generations to be discrete, no clear temporal structure was identified, which could be attributed to the varying duration of larval development. Since population bottlenecks were detected and estimates of effective number of breeders were low, conservation actions are eminent which should include the establishment of suitable dead wood for oviposition on both local and regional scales to increase (re)colonisation success and connectivity among current populations.

Data from: Song structure, not high-frequency song content, determines high-frequency auditory sensitivity in nine species of New World sparrows (Passeriformes: Emberizidae)

1. The evolution of vocal signals can be constrained by a host of factors including habitat effects on sound propagation, morphology of sound-producing structures, and phylogenetic relationships among species. Here, we asked whether auditory sensitivity over a broad range of frequencies correlates with the spectral content of conspecific vocalizations, or whether it is constrained by the overall structure of vocalizations, habitat effects on sound propagation, or relatedness among species. 2. We studied nine New World sparrows (Passeriformes: Emberizidae) including three open-habitat species, three scrub-like habitat species, and three forest species. For each habitat, one species had pure trilled songs, another had tonal songs, and another had complex songs with tones, trills, and amplitude-modulated buzzes. 3. As predicted by the acoustic adaptation hypothesis, song spectral properties (specifically frequency and entropy) had the highest values in open-habitat species and the lowest values in forest species. 4. Based on our results from song analyses, and the sender-receiver matching hypothesis, we predicted that open-habitat species would be more sensitive to high-frequency sounds compared to forest species. Contrary to this prediction, habitat and high-frequency song content had little effect on audiogram shape. Song type, however, had a strong effect, with species that produce complex songs showing higher sensitivity to high-frequency sounds than all other species. 5. Our results suggest that the use of song frequency by receivers depends on song structure and not necessarily on song spectral content. Therefore, our current understanding of how signal-processing mechanisms should match signal properties appears to be too simple. When thinking about the evolution of signal-processing mechanisms, the multidimensionality of signals, and how the different dimensions can interact, should be considered.

Data from: Mechanical incompatibility caused by modifications of multiple male genital structures using genomic introgression in Drosophila

Mechanical incompatibility of male and female genitalia is common in animals with internal fertilization. However, our knowledge regarding the precise mechanisms is limited. One key question regards the susceptibility of the match between male and female genitalia to morphological modification. To address this issue, we generated six different second-chromosome introgression lines possessing partially Drosophila mauritiana-like genital morphology in multiple structures in D. simulans background. Three of the six introgression males showed elevated mobility at some stages during copulation with D. simulans females; this was assumed to be an indication of genital mismatch. Notably, one of the introgression males with D. mauritiana-like enlarged anal plates showed occasional leakage of adhesive ejaculate on the body surface when mated with pure D. simulans females, suggesting apparent structural incompatibility in genital coupling. These observations suggested that both sexual and natural selection shape the anal plate morphology, highlighting the role of this structure as an important component of mechanical isolation. Partial replacement (introgression) by a sibling species genome can induce perturbations in genital coupling mechanics, suggesting that genital compatibility can be susceptible to subtle genomic changes at the early stages of divergence in these species.

opencc-zeroJul 2021View details →

Data from: Fine-scale spatial genetic structure across the species range reflects recent colonization of high elevation habitats in silver fir (Abies alba Mill.)

Variation in genetic diversity across species ranges has long been recognized as highly informative for assessing populations' resilience and adaptive potential. The spatial distribution of genetic diversity within populations, referred to as fine-scale spatial genetic structure (FSGS), also carries information about recent demographic changes, yet it has rarely been connected to range scale processes. We studied eight silver fir (Abies alba Mill.) population pairs (sites), growing at high and low elevations, representative of the main genetic lineages of the species. A total of 1368 adult trees and 540 seedlings were genotyped using 137 and 116 single nucleotide polymorphisms (SNPs), respectively. Sites revealed a clear east-west isolation-by-distance pattern consistent with the post-glacial colonization history of the species. Genetic differentiation among sites (FCT=0.148) was an order of magnitude greater than between elevations within sites (FSC=0.031), nevertheless high elevation populations consistently exhibited a stronger FSGS. Structural equation modeling revealed that elevation and, to a lesser extent, post-glacial colonization history, but not climatic and habitat variables, were the best predictors of FSGS across populations. These results suggest that high elevation habitats have been colonized more recently across the species range. Additionally, paternity analysis revealed a high reproductive skew among adults and a stronger FSGS in seedlings than in adults, suggesting that FSGS may conserve the signature of demographic changes for several generations. Our results emphasize that spatial patterns of genetic diversity within populations provide information about demographic history complementary to non-spatial statistics, and could be used for genetic diversity monitoring, especially in forest trees.

opencc-zeroDec 2016View details →

Data from: Inferring pathobiology from structural MRI in schizophrenia and bipolar disorder: modeling head motion and neuroanatomical specificity

Despite over 400 peer-reviewed structural MRI publications documenting neuroanatomic abnormalities in bipolar disorder and schizophrenia, the confounding effects of head motion and the regional specificity of these defects are unclear. Using a large cohort of individuals scanned on the same research dedicated MRI with broadly similar protocols, we observe reduced cortical thickness indices in both illnesses, though less pronounced in bipolar disorder. While schizophrenia (n = 226) was associated with wide-spread surface area reductions, bipolar disorder (n = 227) and healthy comparison subjects (n = 370) did not differ. We replicate earlier reports that head motion (estimated from time-series data) influences surface area and cortical thickness measurements and demonstrate that motion influences a portion, but not all, of the observed between-group structural differences. Although the effect sizes for these differences were small to medium, when global indices were covaried during vertex-level analyses, between-group effects became nonsignificant. This analysis raises doubts about the regional specificity of structural brain changes, possible in contrast to functional changes, in affective and psychotic illnesses as measured with current imaging technology. Given that both schizophrenia and bipolar disorder showed cortical thickness reductions, but only schizophrenia showed surface area changes, and assuming these measures are influenced by at least partially unique sets of biological factors, then our results could indicate some degree of specificity between bipolar disorder and schizophrenia.

opencc-zeroDec 2014View details →

Data from: How obstacles perturb population fronts and alter their genetic structure

As populations spread into new territory, environmental heterogeneities can shape the population front and genetic composition. We focus here on the effects of an important building block of heterogeneous environments, isolated obstacles. With a combination of experiments, theory, and simulation, we show how isolated obstacles both create long-lived distortions of the front shape and amplify the effect of genetic drift. A system of bacteriophage T7 spreading on a spatially heterogeneous Escherichia coli lawn serves as an experimental model system to study population expansions. Using an inkjet printer, we create well-defined replicates of the lawn and quantitatively study the population expansion of phage T7. The transient perturbations of the population front found in the experiments are well described by a model in which the front moves with constant speed. Independent of the precise details of the expansion, we show that obstacles create a kink in the front that persists over large distances and is insensitive to the details of the obstacle's shape. The small deviations between experimental findings and the predictions of the constant speed model can be understood with a more general reaction-diffusion model, which reduces to the constant speed model when the obstacle size is large compared to the front width. Using this framework, we demonstrate that frontier genotypes just grazing the side of an isolated obstacle increase in abundance, a phenomenon we call 'geometry-enhanced genetic drift', complementary to the founder effect associated with spatial bottlenecks. Bacterial range expansions around nutrient-poor barriers and stochastic simulations confirm this prediction. The effect of the obstacle on the genealogy of individuals at the front is characterized by simulations and rationalized using the constant speed model. Lastly, we consider the effect of two obstacles on front shape and genetic composition of the population illuminating the effects expected from complex environments with many obstacles.

opencc-zeroSep 2016View details →

Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing

Switchgrass (Panicum virgatum L.) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuels feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype composed of tetraploid and octoploid accessions, and a southern lowland ecotype composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data, we identified ~27 million single nucleotide polymorphisms (SNPs), of which 1,590,653 high confidence SNPs were used in downstream analyses of diversity within and between the populations. From the 66 populations, we identified five primary population groups within the upland and lowland ecotypes, a result that was further supported through genetic distance analysis. We identified conserved, ecotype restricted non-synonymous SNPs that are predicted to impact protein function in genes that encode CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes involved in flowering which may contribute to the phenotypic differences between the two ecotypes. We also identified, relative to the near-reference Kanlow population, 17,228 up-copy number variants (CNVs), 112,630 down-CNVs, and 14,430 presence/absence variants (PAV) impacting a total of 9,979 genes, including two upland-specific CNV-clusters. In total, 45,719 genes were impacted by a SNP, CNV, or a PAV across the panel providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.