Socio-technical scales in socio-environmental modeling: Managing a system-of-systems modeling approach.

System-of-systems approaches for integrated assessments have become prevalent in recent years. Such approaches integrate a variety of models from different disciplines and modeling paradigms to represent a socio-environmental (or social-ecological) system aiming to holistically inform policy and decision-making processes. Central to the system-of-systems approaches is the representation of systems in a multi-tier framework with nested scales. Current modeling paradigms, however, have disciplinary-specific lineage, leading to inconsistencies in the conceptualization and integration of socio-environmental systems. In this paper, a multidisciplinary team of researchers, from engineering, natural and social sciences, have come together to detail socio-technical practices and challenges that arise in the consideration of scale throughout the socio-environmental modeling process. We identify key paths forward, focused on explicit consideration of scale and uncertainty, strengthening interdisciplinary communication, and improvement of the documentation process. We call for a grand vision (and commensurate funding) for holistic system-of-systems research that engages researchers, stakeholders, and policy makers in a multi-tiered process for the co-creation of knowledge and solutions to major socio-environmental problems.

Pinaceae show elevated rates of gene turnover that are robust to incomplete gene annotation.

Gene duplications and gene losses are major determinants of genome evolution and phenotypic diversity. The frequency of gene turnover (gene gains and gene losses combined) is known to vary between organisms. Comparative genomic analyses of gene families can highlight such variation; however, estimates of gene turnover may be biased when using highly fragmented genome assemblies resulting in poor gene annotations. Here, we address potential biases introduced by gene annotation errors in estimates of gene turnover frequencies in a dataset including both well-annotated angiosperm genomes and the incomplete gene sets of four Pinaceae, including two pine species, Norway spruce and Douglas-fir. We show that Pinaceae experienced higher gene turnover rates than angiosperm lineages lacking recent whole-genome duplications. This finding is robust to both known major issues in Pinaceae gene sets: missing gene models and erroneous annotation of pseudogenes. A separate analysis limited to the four Pinaceae gene sets pointed to an accelerated gene turnover rate in pines compared with Norway spruce and Douglas-fir. Our results indicate that gene turnover significantly contributes to genome variation and possibly to speciation in Pinaceae, particularly in pines. Moreover, these findings indicate that reliable estimates of gene turnover frequencies can be discerned in incomplete and potentially inaccurate gene sets. Because gymnosperms are known to exhibit low overall substitution rates compared with angiosperms, our results suggest that the rate of single-base pair mutations is uncoupled from the rate of large DNA duplications and deletions associated with gene turnover in Pinaceae.

Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda L.).

BACKGROUND: Loblolly pine (Pinus taeda L.) is one of the most widely planted and commercially important forest tree species in the USA and worldwide, and is an object of intense genomic research. However, whole genome resequencing in loblolly pine is hampered by its large size and complexity and a lack of a good reference. As a valid and more feasible alternative, entire exome sequencing was hence employed to identify the gene-associated single nucleotide polymorphisms (SNPs) and to genotype the sampled trees. RESULTS: The exons were captured in the ADEPT2 association mapping population of 375 clonally-propagated loblolly pine trees using NimbleGen oligonucleotide hybridization probes, and then exome-enriched genomic DNA fragments were sequenced using the Illumina HiSeq 2500 platform. Oligonucleotide probes were designed based on 199,723 exons (≈49 Mbp) partitioned from the loblolly pine reference genome (PineRefSeq v. 1.01). The probes covered 90.2 % of the target regions. Capture efficiency was high; on average, 67 % of the sequence reads generated for each tree could be mapped to the capture target regions, and more than 70 % of the captured target bases had at least 10X sequencing depth per tree. A total of 972,720 high quality SNPs were identified after filtering. Among them, 53 % were located in coding regions (CDS), 5 % in 5' or 3' untranslated regions (UTRs) and 42 % in non-target and non-coding regions, such as introns and adjacent intergenic regions collaterally captured. We found that linkage disequilibrium (LD) decayed very rapidly, with the correlation coefficient (r (2)) between pairs of SNPs linked within single scaffolds decaying to half maximum (r (2) = 0.22) within 55 bp, to r (2) = 0.1 within 192 bp, and to r (2) = 0.05 within 451 bp. Population structure analysis using unlinked SNPs demonstrated the presence of two main distinct clusters representing western and eastern parts of the loblolly pine range included in our sample of trees. CONCLUSIONS: The obtained results demonstrated the efficiency of exome capture for genotyping species such as loblolly pine with a large and complex genome. The highly diverse genetic variation reported in this study will be a valuable resource for future genetic and genomic research in loblolly pine.

Evaluation of Areawide Forecasts of Wind-borne Crop Pests: Sugarcane Aphid (Hemiptera: Aphididae) Infestations of Sorghum in the Great Plains of North America.

Airborne pests pose a major challenge in agriculture. Integrated pest management programs have been considered a viable response to this challenge, and pest forecasting can aid in strategic management decisions. Annually recurrent areawide sugarcane aphid [Melanaphis sacchari (Zehntner) (Hemiptera: Aphididae)] infestations of sorghum [Sorghum bicolor (L.) Moench (Poales: Poaceae)] in the Great Plains of North America is one of such challenges. As part of the response, a spatially-explicit individual-based model was developed that simulates sugarcane aphid infestations over the southern-to-central part of the region. In this work, we evaluated model forecasts using 2015-2018 field data. The ranges of forecasted days of first infestation significantly overlapped with those observed in the field. The average days of first infestation observed in the field were approximated by the model with differences of less than 28 days in Texas and southern Oklahoma (2015-2018), and in northern Oklahoma (2016-2017). In half of these cases the difference was less than 14 days. In general, the modeled average day of first infestation was earlier than the observed one. As conceptual modeling decisions may impact model forecasts and as various socio-environmental factors may impact spatio-temporal patterns of field data collection, agreement between the forecasts and the observed estimates may vary between locations and seasons. Predictive modeling has the potential to occupy a central position within areawide integrated pest management programs. More detailed consideration of local agricultural practices and local environmental conditions could improve forecasting accuracy, as could broader participation of producers in field monitoring efforts.

Natural Enemies, Mediated by Landscape and Weather Conditions, Shape Response of the Sorghum Agroecosystem of North America to the Invasive Aphid Melanaphis sorghi.

The sorghum (Sorghum bicolor [L.]) agroecosystem of North America provided an opportunity to evaluate agroecosystem response to an invading insect herbivore, Melanaphis sorghi (Theobald) (sorghum aphid) (previously published as Melanaphis sacchari Zehntner) (Hemiptera: Aphididae) onto a widely planted crop that experiences a range of agro-landscape and weather conditions. Initial sorghum risk assessments after M. sorghi's invasion in the mid-2010s provided forecasts of range expansion and annual migration, which were based on aphid life history, extent of sorghum cultivation and susceptibility to M. sorghi, and weather (aphid-plant-weather [APW] risk scenario). A more comprehensive risk assessment proposed here brings top-down forces of M. sorghi-natural enemy interactions to the forefront as mediated by agro-landscape and weather conditions (aphid-enemy/landscape-weather mediated [AE/LW] risk scenario). A hypothesis of regional differences in aphids and natural enemies and sensitivity to agro-landscape and weather was tested using empirical data of insect, landscape, and weather data across 5 years and four regions (two in the U.S. Great Plains [South GP and North GP], one farther south (South), and one in the southeast U.S. [South E]). Natural enemies were widespread with two parasitoids and four coccinellid species common across regions, but regional variation in M. sorghi and natural enemy abundance was detected. The AE/LW risk scenario accounted for natural enemy abundance and activity that was highest in the South region, functioned well across agro-landscape and weather conditions, and was accompanied by average low M. sorghi abundance (~23 M. sorghi per leaf). Positive correlations of natural enemy-M. sorghi abundance also occurred in the South GP region where M. sorghi abundance was low (~20 M. sorghi per leaf), and selected natural enemy activity appeared to be mediated by landscape composition. Melanaphis sorghi abundance was highest in the South E region (~136 aphids/leaf) where natural enemy activity was low and influenced by weather. The AE/LW risk scenario appeared suited, and essential in the South region, in assessing risk on a regional scale, and sets the stage for further modeling to generate estimates of the degree of influence of natural enemies under varying agro-landscape and weather conditions considered in the AE/LW risk scenario. Broadly, these findings are relevant in understanding agroecosystem resilience and recommending supportive management inputs in response to insect invasions in context of natural enemy activity and varied environmental conditions.

Understory upheaval: factors influencing Japanese stiltgrass invasion in forestlands of Tennessee, United States.

BACKGROUND: Invasions by non-native plants contribute to loss of ecosystem biodiversity and productivity, modification of biogeochemical cycles, and inhibition of natural regeneration of native species. Japanese stiltgrass (Microstegium vimineum (Trin.) A. Campus) is one of the most prevalent invasive grasses in the forestlands of Tennessee, United States. We measured the extent of invasion, identified potential factors affecting invasion, and quantified the relative importance of each factor. We analyzed field data collected by the Forest Inventory and Analysis Program of the U.S. Forest Service to measure the extent of invasion from 2005 to 2011 and identified potential factors affecting invasion during this period using boosted regression trees. RESULTS: Our results indicated that presence of Japanese stiltgrass on sampled plots increased 50% (from 269 to 404 plots) during the time period. The probability of invasion was correlated with one landscape condition (elevation) (20.5%) and five forest features (including tree species diversity, basal area, stand age, site productivity, and natural regeneration) (79.5%). Boosted regression trees identified the most influential (highly correlated) variables as tree species diversity (30.7%), basal area (22.9%), elevation (20.5%), and stand age (16.7%). Our results suggest that Japanese stiltgrass is likely to continue its invasion in Tennessee forests. CONCLUSIONS: The present model, in addition to correlating the probability of Japanese stiltgrass invasions with current climatic conditions and landscape attributes, could aid in the on-going development of control strategies for confronting Japanese stiltgrass invasions by identifying vulnerable areas that might emerge as a result of likely changes in climatic conditions and land use patterns.

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.

A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50 = 340,704 bp). Incremental improvements in sequencing and assembly technologies are in part responsible for the higher quality reference genome, but it may also be due to a slightly lower exact repeat content in Douglas-fir vs. pine and spruce. Comparative genome annotation with angiosperm species reveals gene-family expansion and contraction in Douglas-fir and other conifers which may account for some of the major morphological and physiological differences between the two major plant groups. Notable differences in the size of the NDH-complex gene family and genes underlying the functional basis of shade tolerance/intolerance were observed. This reference genome sequence not only provides an important resource for Douglas-fir breeders and geneticists but also sheds additional light on the evolutionary processes that have led to the divergence of modern angiosperms from the more ancient gymnosperms.

Conflicting genomic signals affect phylogenetic inference in four species of North American pines.

Adaptive evolutionary processes in plants may be accompanied by episodes of introgression, parallel evolution and incomplete lineage sorting that pose challenges in untangling species evolutionary history. Genus Pinus (pines) is one of the most abundant and most studied groups among gymnosperms, and a good example of a lineage where these phenomena have been observed. Pines are among the most ecologically and economically important plant species. Some, such as the pines of the southeastern USA (southern pines in subsection Australes), are subjects of intensive breeding programmes. Despite numerous published studies, the evolutionary history of Australes remains ambiguous and often controversial. We studied the phylogeny of four major southern pine species: shortleaf (Pinus echinata), slash (P. elliottii), longleaf (P. palustris) and loblolly (P. taeda), using sequences from 11 nuclear loci and maximum likelihood and Bayesian methods. Our analysis encountered resolution difficulties similar to earlier published studies. Although incomplete lineage sorting and introgression are two phenomena presumptively underlying our results, the phylogenetic inferences seem to be also influenced by the genes examined, with certain topologies supported by sets of genes sharing common putative functionalities. For example, genes involved in wood formation supported the clade echinata-taeda, genes linked to plant defence supported the clade echinata-elliottii and genes linked to water management properties supported the clade echinata-palustris The support for these clades was very high and consistent across methods. We discuss the potential factors that could underlie these observations, including incomplete lineage sorting, hybridization and parallel or adaptive evolution. Our results likely reflect the relatively short evolutionary history of the subsection that is thought to have begun during the middle Miocene and has been influenced by climate fluctuations.

Integrating spread dynamics and economics of timber production to manage Chinese tallow invasions in southern U.S. forestlands.

Economic costs associated with the invasion of nonnative species are of global concern. We estimated expected costs of Chinese tallow (Triadica sebifera (L.) Small) invasions related to timber production in southern U.S. forestlands under different management strategies. Expected costs were confined to the value of timber production losses plus costs for search and control. We simulated management strategies including (1) no control (NC), and control beginning as soon as the percentage of invaded forest land exceeded (2) 60 (Low Control), (3) 25 (Medium Control), or (4) 0 (High Control) using a spatially-explicit, stochastic, bioeconomic model. With NC, simulated invasions spread northward and westward into Arkansas and along the Gulf of Mexico to occupy ≈1.2 million hectares within 20 years, with associated expected total costs increasing exponentially to ≈$300 million. With LC, MC, and HC, invaded areas reached ≈275, 34, and 2 thousand hectares after 20 years, respectively, with associated expected costs reaching ≈$400, $230, and $200 million. Complete eradication would not be cost-effective; the minimum expected total cost was achieved when control began as soon as the percentage of invaded land exceeded 5%. These results suggest the importance of early detection and control of Chinese tallow, and emphasize the importance of integrating spread dynamics and economics to manage invasive species.

Evolution of exon-intron structure and alternative splicing.

Despite significant advances in high-throughput DNA sequencing, many important species remain understudied at the genome level. In this study we addressed a question of what can be predicted about the genome-wide characteristics of less studied species, based on the genomic data from completely sequenced species. Using NCBI databases we performed a comparative genome-wide analysis of such characteristics as alternative splicing, number of genes, gene products and exons in 36 completely sequenced model species. We created statistical regression models to fit these data and applied them to loblolly pine (Pinus taeda L.), an example of an important species whose genome has not been completely sequenced yet. Using these models, the genome-wide characteristics, such as total number of genes and exons, can be roughly predicted based on parameters estimated from available limited genomic data, e.g. exon length and exon/gene ratio.

Parentage versus two-generation analyses for estimating pollen-mediated gene flow in plant populations.

Assessment of contemporary pollen-mediated gene flow in plants is important for various aspects of plant population biology, genetic conservation and breeding. Here, through simulations we compare the two alternative approaches for measuring pollen-mediated gene flow: (i) the NEIGHBORHOOD model--a representative of parentage analyses, and (ii) the recently developed TWOGENER analysis of pollen pool structure. We investigate their properties in estimating the effective number of pollen parents (N(ep)) and the mean pollen dispersal distance (delta). We demonstrate that both methods provide very congruent estimates of N(ep) and delta, when the methods' assumptions considering the shape of pollen dispersal curve and the mating system follow those used in data simulations, although the NEIGHBORHOOD model exhibits generally lower variances of the estimates. The violations of the assumptions, especially increased selfing or long-distance pollen dispersal, affect the two methods to a different degree; however, they are still capable to provide comparable estimates of N(ep). The NEIGHBORHOOD model inherently allows to estimate both self-fertilization and outcrossing due to the long-distance pollen dispersal; however, the TWOGENER method is particularly sensitive to inflated selfing levels, which in turn may confound and suppress the effects of distant pollen movement. As a solution we demonstrate that in case of TWOGENER it is possible to extract the fraction of intraclass correlation that results from outcrossing only, which seems to be very relevant for measuring pollen-mediated gene flow. The two approaches differ in estimation precision and experimental efforts but they seem to be complementary depending on the main research focus and type of a population studied.