Correspondence

quantification, real-time PCR, rumen, stearic acid producers

Polyploid plants have faster rates of multivariate niche differentiation than their diploid relatives

Polyploid speciation entails substantial and rapid postzygotic reproductive isolation of nascent species that are initially sympatric with one or both parents. Despite strong postzygotic isolation, ecological niche differentiation has long been thought to be important for polyploid success. Using biogeographic data from across vascular plants, we tested whether the climatic niches of polyploid species are more differentiated than their diploid relatives and if the climatic niches of polyploid species differentiated faster than those of related diploids. We found that polyploids are often more climatically differentiated from their diploid parents than the diploids are from each other. Consistent with this pattern, we estimated that polyploid species generally have higher rates of multivariate niche differentiation than their diploid relatives. In contrast to recent analyses, our results confirm that ecological niche differentiation is an important component of polyploid speciation and that niche differentiation is often significantly faster in polyploids.Polyploid speciation entails substantial and rapid postzygotic reproductive isolation of nascent species that are initially sympatric with one or both parents. Despite strong postzygotic isolation, ecological niche differentiation has long been thought to be important for polyploid success. Using biogeographic data from across vascular plants, we tested whether the climatic niches of polyploid species are more differentiated than their diploid relatives and if the climatic niches of polyploid species differentiated faster than those of related diploids.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/153074/1/ele13402-sup-0001-TableS1.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153074/2/ele13402_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153074/3/ele13402-sup-0007-TableS7.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153074/4/ele13402-sup-0003-TableS3.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153074/5/ele13402-sup-0005-TableS5.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153074/6/ele13402.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153074/7/ele13402-sup-0006-TableS6.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153074/8/ele13402-sup-0002-TableS2.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153074/9/ele13402-sup-0004-TableS4.pd

A genome triplication associated with early diversification of the core eudicots

Background: Although it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear. Results: To determine when this polyploidization occurred relative to speciation events in angiosperm history, we employed a phylogenomic approach to investigate the timing of gene set duplications located on syntenic gamma blocks. We populated 769 putative gene families with large sets of homologs obtained from public transcriptomes of basal angiosperms, magnoliids, asterids, and more than 91.8 gigabases of new next-generation transcriptome sequences of non-grass monocots and basal eudicots. The overwhelming majority (95%) of well-resolved gamma duplications was placed before the separation of rosids and asterids and after the split of monocots and eudicots, providing strong evidence that the gamma polyploidy event occurred early in eudicot evolution. Further, the majority of gene duplications was placed after the divergence of the Ranunculales and core eudicots, indicating that the gamma appears to be restricted to core eudicots. Molecular dating estimates indicate that the duplication events were intensely concentrated around 117 million years ago. Conclusions: The rapid radiation of core eudicot lineages that gave rise to nearly 75% of angiosperm species appears to have occurred coincidentally or shortly following the gamma triplication event. Reconciliation of gene trees with a species phylogeny can elucidate the timing of major events in genome evolution, even when genome sequences are only available for a subset of species represented in the gene trees. Comprehensive transcriptome datasets are valuable complements to genome sequences for high-resolution phylogenomic analysis

Global Atmospheric Budget of Acetone: Air-Sea Exchange and the Contribution to Hydroxyl Radicals

Acetone is one of the most abundant oxygenated volatile organic compounds (VOCs) in the atmosphere. The oceans impose a strong control on atmospheric acetone, yet the oceanic fluxes of acetone remain poorly constrained. In this work, the global budget of acetone is evaluated using two global models: CAM‐chem and GEOS‐Chem. CAM‐chem uses an online air‐sea exchange framework to calculate the bidirectional oceanic acetone fluxes, which is coupled to a data‐oriented machine‐learning approach. The machine‐learning algorithm is trained using a global suite of seawater acetone measurements. GEOS‐Chem uses a fixed surface seawater concentration of acetone to calculate the oceanic fluxes. Both model simulations are compared to airborne observations from a recent global‐scale, multiseasonal campaign, the NASA Atmospheric Tomography Mission (ATom). We find that both CAM‐chem and GEOS‐Chem capture the measured acetone vertical distributions in the remote atmosphere reasonably well. The combined observational and modeling analysis suggests that (i) the ocean strongly regulates the atmospheric budget of acetone. The tropical and subtropical oceans are mostly a net source of acetone, while the high‐latitude oceans are a net sink. (ii) CMIP6 anthropogenic emission inventory may underestimate acetone and/or its precursors in the Northern Hemisphere. (iii) The MEGAN biogenic emissions model may overestimate acetone and/or its precursors, and/or the biogenic oxidation mechanisms may overestimate the acetone yields. (iv) The models consistently overestimate acetone in the upper troposphere‐lower stratosphere over the Southern Ocean in austral winter. (v) Acetone contributes up to 30–40% of hydroxyl radical production in the tropical upper troposphere/lower stratosphere

Aircraft-based inversions quantify the importance of wetlands and livestock for Upper Midwest methane emissions

We apply airborne measurements across three seasons (summer, winter and spring 2017-2018) in a multi-inversion framework to quantify methane emissions from the US Corn Belt and Upper Midwest, a key agricultural and wetland source region. Combing our seasonal results with prior fall values we find that wetlands are the largest regional methane source (32 %, 20 [16-23] Gg/d), while livestock (enteric/manure; 25 %, 15 [14-17] Gg/d) are the largest anthropogenic source. Natural gas/petroleum, waste/landfills, and coal mines collectively make up the remainder. Optimized fluxes improve model agreement with independent datasets within and beyond the study timeframe. Inversions reveal coherent and seasonally dependent spatial errors in the WetCHARTs ensemble mean wetland emissions, with an underestimate for the Prairie Pothole region but an overestimate for Great Lakes coastal wetlands. Wetland extent and emission temperature dependence have the largest influence on prediction accuracy; better representation of coupled soil temperature-hydrology effects is therefore needed. Our optimized regional livestock emissions agree well with the Gridded EPA estimates during spring (to within 7 %) but are g≈ 25 % higher during summer and winter. Spatial analysis further shows good top-down and bottom-up agreement for beef facilities (with mainly enteric emissions) but larger (g≈ 30 %) seasonal discrepancies for dairies and hog farms (with \u3e 40 % manure emissions). Findings thus support bottom-up enteric emission estimates but suggest errors for manure; we propose that the latter reflects inadequate treatment of management factors including field application. Overall, our results confirm the importance of intensive animal agriculture for regional methane emissions, implying substantial mitigation opportunities through improved management

Global Atmospheric Budget of Acetone: Air‐Sea Exchange and the Contribution to Hydroxyl Radicals

Acetone is one of the most abundant oxygenated volatile organic compounds (VOCs) in the atmosphere. The oceans impose a strong control on atmospheric acetone, yet the oceanic fluxes of acetone remain poorly constrained. In this work, the global budget of acetone is evaluated using two global models: CAM‐chem and GEOS‐Chem. CAM‐chem uses an online air‐sea exchange framework to calculate the bidirectional oceanic acetone fluxes, which is coupled to a data‐oriented machine‐learning approach. The machine‐learning algorithm is trained using a global suite of seawater acetone measurements. GEOS‐Chem uses a fixed surface seawater concentration of acetone to calculate the oceanic fluxes. Both model simulations are compared to airborne observations from a recent global‐scale, multiseasonal campaign, the NASA Atmospheric Tomography Mission (ATom). We find that both CAM‐chem and GEOS‐Chem capture the measured acetone vertical distributions in the remote atmosphere reasonably well. The combined observational and modeling analysis suggests that (i) the ocean strongly regulates the atmospheric budget of acetone. The tropical and subtropical oceans are mostly a net source of acetone, while the high‐latitude oceans are a net sink. (ii) CMIP6 anthropogenic emission inventory may underestimate acetone and/or its precursors in the Northern Hemisphere. (iii) The MEGAN biogenic emissions model may overestimate acetone and/or its precursors, and/or the biogenic oxidation mechanisms may overestimate the acetone yields. (iv) The models consistently overestimate acetone in the upper troposphere‐lower stratosphere over the Southern Ocean in austral winter. (v) Acetone contributes up to 30–40% of hydroxyl radical production in the tropical upper troposphere/lower stratosphere

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B 12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents â 1/475% of the genus-level bacterial and archaeal taxa present in the rumen. © 2018 Nature Publishing Group. All rights reserved

Single Nucleotide Polymorphism–based Genetic Diversity in the Reference Set of Peanut (Arachis spp.) by Developing and Applying Cost-Effective Kompetitive Allele Specific Polymerase Chain Reaction Genotyping Assays

Kompetitive allele-specific polymerase chain reaction (KASP) assays have emerged as cost-effective marker assays especially for molecular breeding applications. Therefore, a set of 96 informative single nucleotide polymorphisms (SNPs) was used to develop KASP assays in groundnut or peanut (Arachis spp.). Developed assays were designated as groundnut KASP assay markers (GKAMs) and screened on 94 genotypes (validation set) that included parental lines of 27 mapping populations, seven synthetic autotetraploid and amphidiploid lines, and 19 wild species accessions. As a result, 90 GKAMs could be validated and 73 GKAMs showed polymorphism in the validation set. Validated GKAMs were screened on 280 diverse genotypes of the reference set for estimating diversity features and elucidating genetic relationships. Cluster analysis of marker allelic data grouped accessions according to their genome type, subspecies, and botanical variety. The subspecies Arachis hypogaea L. subsp. fastigiata Waldron and A. hypogaea subsp. hypogaea formed distinct cluster; however, some overlaps were found indicating their frequent intercrossing during the course of evolution. The wild species, having diploid genomes, were grouped into a single cluster. The average polymorphism information content value for polymorphic GKAMs was 0.32 in the validation set and 0.31 in the reference set. These validated and highly informative GKAMs may be useful for genetics and breeding applications in Arachis species

Global Atmospheric Budget of Acetone: Air‐Sea Exchange and the Contribution to Hydroxyl Radicals

Acetone is one of the most abundant oxygenated volatile organic compounds (VOCs) in the atmosphere. The oceans impose a strong control on atmospheric acetone, yet the oceanic fluxes of acetone remain poorly constrained. In this work, the global budget of acetone is evaluated using two global models: CAM‐chem and GEOS‐Chem. CAM‐chem uses an online air‐sea exchange framework to calculate the bidirectional oceanic acetone fluxes, which is coupled to a data‐oriented machine‐learning approach. The machine‐learning algorithm is trained using a global suite of seawater acetone measurements. GEOS‐Chem uses a fixed surface seawater concentration of acetone to calculate the oceanic fluxes. Both model simulations are compared to airborne observations from a recent global‐scale, multiseasonal campaign, the NASA Atmospheric Tomography Mission (ATom). We find that both CAM‐chem and GEOS‐Chem capture the measured acetone vertical distributions in the remote atmosphere reasonably well. The combined observational and modeling analysis suggests that (i) the ocean strongly regulates the atmospheric budget of acetone. The tropical and subtropical oceans are mostly a net source of acetone, while the high‐latitude oceans are a net sink. (ii) CMIP6 anthropogenic emission inventory may underestimate acetone and/or its precursors in the Northern Hemisphere. (iii) The MEGAN biogenic emissions model may overestimate acetone and/or its precursors, and/or the biogenic oxidation mechanisms may overestimate the acetone yields. (iv) The models consistently overestimate acetone in the upper troposphere‐lower stratosphere over the Southern Ocean in austral winter. (v) Acetone contributes up to 30–40% of hydroxyl radical production in the tropical upper troposphere/lower stratosphere