Integrating forest structural diversity measurement into ecological research

The measurement of forest structure has evolved steadily due to advances in technology, methodology, and theory. Such advances have greatly increased our capacity to describe key forest structural elements and resulted in a range of measurement approaches from traditional analog tools such as measurement tapes to highly derived and computationally intensive methods such as advanced remote sensing tools (e.g., lidar, radar). This assortment of measurement approaches results in structural metrics unique to each method, with the caveat that metrics may be biased or constrained by the measurement approach taken. While forest structural diversity (FSD) metrics foster novel research opportunities, understanding how they are measured or derived, limitations of the measurement approach taken, as well as their biological interpretation is crucial for proper application. We review the measurement of forest structure and structural diversity—an umbrella term that includes quantification of the distribution of functional and biotic components of forests. We consider how and where these approaches can be used, the role of technology in measuring structure, how measurement impacts extend beyond research, and current limitations and potential opportunities for future research

A theoretical framework for the ecological role of three-dimensional structural diversity

The three-dimensional (3D) physical aspects of ecosystems are intrinsically linked to ecological processes. Here, we describe structural diversity as the volumetric capacity, physical arrangement, and identity/traits of biotic components in an ecosystem. Despite being recognized in earlier ecological studies, structural diversity has been largely overlooked due to an absence of not only a theoretical foundation but also effective measurement tools. We present a framework for conceptualizing structural diversity and suggest how to facilitate its broader incorporation into ecological theory and practice. We also discuss how the interplay of genetic and environmental factors underpin structural diversity, allowing for a potentially unique synthetic approach to explain ecosystem function. A practical approach is then proposed in which scientists can test the ecological role of structural diversity at biotic–environmental interfaces, along with examples of structural diversity research and future directions for integrating structural diversity into ecological theory and management across scales

Expression of APOBEC3G/3F and G-to-A Hypermutation Levels in HIV-1-Infected Children with Different Profiles of Disease Progression

OBJECTIVE: Increasing evidence has accumulated showing the role of APOBEC3G (A3G) and 3F (A3F) in the control of HIV-1 replication and disease progression in humans. However, very few studies have been conducted in HIV-infected children. Here, we analyzed the levels of A3G and A3F expression and induced G-to-A hypermutation in a group of children with distinct profiles of disease progression. METHODOLOGY/PRINCIPAL FINDINGS: Perinatally HIV-infected children were classified as progressors or long-term non-progressors according to criteria based on HIV viral load and CD4 T-cell counts over time. A group of uninfected control children were also enrolled in the study. PBMC proviral DNA was assessed for G-to-A hypermutation, whereas A3G and A3F mRNA were isolated and quantified through TaqMan® real-time PCR. No correlation was observed between disease progression and A3G/A3F expression or hypermutation levels. Although all children analyzed showed higher expression levels of A3G compared to A3F (an average fold of 5 times), a surprisingly high A3F-related hypermutation rate was evidenced in the cohort, irrespective of the child's disease progression profile. CONCLUSION: Our results contribute to the current controversy as to whether HIV disease progression is related to A3G/A3F enzymatic activity. To our knowledge, this is the first study analyzing A3G/F expression in HIV-infected children, and it may pave the way to a better understanding of the host factors governing HIV disease in the pediatric setting

HLA class I and II diversity contributes to the etiologic heterogeneity of non-Hodgkin lymphoma subtypes

A growing number of loci within the human leukocyte antigen (HLA) region have been implicated in non-Hodgkin lymphoma (NHL) etiology. Here, we test a complementary hypothesis of "heterozygote advantage" regarding the role of HLA and NHL, whereby HLA diversity is beneficial and homozygous HLA loci are associated with increased disease risk. HLA alleles at class I and II loci were imputed from genome-wide association studies (GWAS) using SNP2HLA for: 3,617 diffuse large B-cell lymphomas (DLBCL), 2,686 follicular lymphomas (FL), 2,878 chronic lymphocytic leukemia/small lymphocytic lymphomas (CLL/SLL), 741 marginal zone lymphomas (MZL), and 8,753 controls of European descent. Both DLBCL and MZL risk were elevated with homozygosity at class I HLA-B and -C loci (OR DLBCL=1.31, 95% CI=1.06-1.60; OR MZL=1.45, 95% CI=1.12-1.89) and class II HLA-DRB1 locus (OR DLBCL=2.10, 95% CI=1.24-3.55; OR MZL= 2.10, 95% CI=0.99-4.45). Increased FL risk was observed with the overall increase in number of homozygous HLA class II loci (p-trend<0.0001, FDR=0.0005). These results support a role for HLA zygosity in NHL etiology and suggests that distinct immune pathways may underly the etiology of the different NHL subtypes

Harnessing the NEON data revolution to advance open environmental science with a diverse and data-capable community

It is a critical time to reflect on the National Ecological Observatory Network (NEON) science to date as well as envision what research can be done right now with NEON (and other) data and what training is needed to enable a diverse user community. NEON became fully operational in May 2019 and has pivoted from planning and construction to operation and maintenance. In this overview, the history of and foundational thinking around NEON are discussed. A framework of open science is described with a discussion of how NEON can be situated as part of a larger data constellation—across existing networks and different suites of ecological measurements and sensors. Next, a synthesis of early NEON science, based on >100 existing publications, funded proposal efforts, and emergent science at the very first NEON Science Summit (hosted by Earth Lab at the University of Colorado Boulder in October 2019) is provided. Key questions that the ecology community will address with NEON data in the next 10 yr are outlined, from understanding drivers of biodiversity across spatial and temporal scales to defining complex feedback mechanisms in human–environmental systems. Last, the essential elements needed to engage and support a diverse and inclusive NEON user community are highlighted: training resources and tools that are openly available, funding for broad community engagement initiatives, and a mechanism to share and advertise those opportunities. NEON users require both the skills to work with NEON data and the ecological or environmental science domain knowledge to understand and interpret them. This paper synthesizes early directions in the community’s use of NEON data, and opportunities for the next 10 yr of NEON operations in emergent science themes, open science best practices, education and training, and community building

Hybrid Watermilfoil Lineages are More Invasive and Less Sensitive to a Commonly used Herbicide than their Exotic Parent (Eurasian watermilfoil)

Hybridization may stimulate the evolution of invasiveness in human-impacted habitats if unique hybrid genotypes have higher fitness than parental genotypes. Human efforts to control invasive taxa frequently involve the intentional alteration of habitats, but few studies have considered whether hybridization can result in decreased sensitivity to control measures. Here, we investigate whether interspecific hybrids between introduced Eurasian watermilfoil (Myriophyllum spicatum) and native northern watermilfoil (M. sibiricum) are more invasive than parental Eurasian watermilfoil, especially in regard to their relative responses to an herbicide commonly applied for their control (2,4-dichlorophenoxyacetic acid; 2,4-D). In two separate laboratory experiments, hybrids on average grew faster and were less sensitive to 2,4-D compared with parental Eurasian watermilfoil. These two invasive traits appear to be common in hybrid watermilfoils, as opposed to being restricted to a few unique lineages, because they were found in a diversity of hybrid genotypes from several independent hybridization events. In addition, we found that hybrids occurred more frequently than parental species in natural lakes previously treated with 2,4-D. Our results provide compelling empirical evidence that hybridization is associated with the evolution of increased invasiveness in watermilfoils, and have important implications for their management

Population Structure of the Invasive Round Goby in Lake Michigan

The recent establishment of the round goby (Neogobius melanostomus), an invasive fish in Lake Michigan, provides a model system to view fine scale evolutionary and ecological processes that can create genetic structure within a population. We used seven nuclear polymorphic microsatellite markers (N = 11-17 per site) and measurements of fish total length, weight, and sex (N = 20-74 per site) on round gobies captured by minnow traps and angling among 12 sites around the entire shore of Lake Michigan to determine if evolutionary processes are present in Lake Michigan by characterizing population structure of the round goby. Specific objectives were to determine whether: 1) there are significant patterns of genetic population structure among sites along the shore of Lake Michigan (e.g., a correlation between genetic diversity and geographic distance), 2) ferry shipping routes create strong deviations from normal population structure observed to occur around the lakeshore, and 3) density, fish size, and condition at the 12 sites differ from each other. Results include: significant pairwise FST values, a pattern of isolation by distance (IBD) along the eastern and western shores of Lake Michigan, no IBD along the entire lakeshore, northern, or southern shores, different catch per unit effort (CPUE) and mean weight between sites. A length/weight relationship between fish at all 12 sites was not different. Results indicate that round goby pierhead sites exhibit population structure in Lake Michigan

Hard to Kill: Hybrid Watermilfoil are Less Sensitive to a Commonly Used Herbicide

PURPOSE: The Eurasian watermilfoil and its hybrid with native northern watermilfoil are both widespread invaders that are extensively managed with herbicides. Recent reports by lake managers suggest this hybrid does not respond as well to commonly used herbicides, but very few studies have tested whether or not hybrids are less susceptible to herbicides. In the Menominee River Watershed, in the Western Upper Peninsula of Michigan, hybrids occur more often than parental species in herbicide (2,4-D) treated lakes than untreated lakes. This suggests hybrids may have a competitive advantage in environments where herbicides are commonly used. To test the hypothesis that hybrids are less 2,4-D susceptible than Eurasian watermilfoil, we conducted a herbicide sensitivity assay. SUBJECTS: We experimentally compared 2,4-D sensitivity of six hybrid and four Eurasian watermilfoil populations from the Menominee River Watershed, in addition to a second experiment where we compared 2,4-D sensitivity of six hybrid and nine Eurasian watermilfoil populations from the Lower Peninsula of Michigan. METHODS AND MATERIALS: 2,4-D sensitivity assays were conducted in mesocosms. ANALYSES: A two-way nested analysis of variance was used to compared hybrid and Eurasian watermilfoil 2,4-D sensitivity. RESULTS: Hybrids were less sensitive to 2, 4-D than Eurasian watermilfoil. CONCLUSIONS: If hybrids are less likely to respond to commonly used herbicides, new management strategies may be needed to increase the efficiency of chemical usage in freshwater ecosystems

Structural diversity as a predictor of ecosystem function

Biodiversity is believed to be closely related to ecosystem functions. However, the ability of existing biodiversity measures, such as species richness and phylogenetic diversity, to predict ecosystem functions remains elusive. Here, we propose a new vector of diversity metrics, structural diversity, which directly incorporates niche space in measuring ecosystem structure. We hypothesize that structural diversity will provide better predictive ability of key ecosystem functions than traditional biodiversity measures. Using the new lidar-derived canopy structural diversity metrics on 19 National Ecological Observation Network forested sites across the USA, we show that structural diversity is a better predictor of key ecosystem functions, such as productivity, energy, and nutrient dynamics than existing biodiversity measures (i.e. species richness and phylogenetic diversity). Similar to existing biodiversity measures, we found that the relationships between structural diversity and ecosystem functions are sensitive to environmental context. Our study indicates that structural diversity may be as good or a better predictor of ecosystem functions than species richness and phylogenetic diversity