Sources of inversion variation in the small single copy (SSC) region of chloroplast genomes

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141571/1/ajb21751.pd

Climate and air quality impacts due to mitigation of non-methane near-term climate forcers

It is important to understand how future environmental policies will impact both climate change and air pollution. Although targeting near-term climate forcers (NTCFs), defined here as aerosols, tropospheric ozone, and precursor gases, should improve air quality, NTCF reductions will also impact climate. Prior assessments of the impact of NTCF mitigation on air quality and climate have been limited. This is related to the idealized nature of some prior studies, simplified treatment of aerosols and chemically reactive gases, as well as a lack of a sufficiently large number of models to quantify model diversity and robust responses. Here, we quantify the 2015-2055 climate and air quality effects of non-methane NTCFs using nine state-of-the-art chemistry-climate model simulations conducted for the Aerosol and Chemistry Model Intercomparison Project (AerChemMIP). Simulations are driven by two future scenarios featuring similar increases in greenhouse gases (GHGs) but with weak (SSP3-7.0) versus strong (SSP3-7.0-lowNTCF) levels of air quality control measures. As SSP3-7.0 lacks climate policy and has the highest levels of NTCFs, our results (e.g., surface warming) represent an upper bound. Unsurprisingly, we find significant improvements in air quality under NTCF mitigation (strong versus weak air quality controls). Surface fine particulate matter (PM2:5) and ozone (O3) decrease by 2:20:32 ugm3 and 4:60:88 ppb, respectively (changes quoted here are for the entire 2015-2055 time period; uncertainty represents the 95% confidence interval), over global land surfaces, with larger reductions in some regions including south and southeast Asia. Non-methane NTCF mitigation, however, leads to additional climate change due to the removal of aerosol which causes a net warming effect, including global mean surface temperature and precipitation increases of 0:250:12K and 0:030:012mmd1, respectively. Similarly, increases in extreme weather indices, including the hottest and wettest days, also occur. Regionally, the largest warming and wetting occurs over Asia, including central and north Asia (0:660:20K and 0:030:02mmd1), south Asia (0:470:16K and 0:170:09mmd1), and east Asia (0:460:20K and 0:150:06mmd1). Relatively large warming and wetting of the Arctic also occur at 0:590:36K and 0:040:02mmd1, respectively. Similar surface warming occurs in model simulations with aerosol-only mitigation, implying weak cooling due to ozone reductions. Our findings suggest that future policies that aggressively target non-methane NTCF reductions will improve air quality but will lead to additional surface warming, particularly in Asia and the Arctic. Policies that address other NTCFs including methane, as well as carbon dioxide emissions, must also be adopted to meet climate mitigation goals. © Author(s) 2020. This work is distributed under the Creative Commons Attribution 4.0 License

Reconstructing the basal angiosperm phylogeny: evaluating information content of mitochondrial genes

Three mitochondrial (atp1, matR, nad5), four chloroplast (atpB, matK, rbcL, rpoC2), and one nuclear (18S) genes from 162 seed plants, representing all major lineages of gymnosperms and angiosperms, were analyzed together in a supermatrix or in various partitions using likelihood and parsimony methods. The results show that Amborella + Nymphaeales together constitute the first diverging lineage of angiosperms, and that the topology of Amborella alone being sister to all other angiosperms likely represents a local long branch attraction artifact. The monophyly of magnoliids, as well as sister relationships between Magnoliales and Laurales, and between Canellales and Piperales, are all strongly supported. The sister relationship to eudicots of Ceratophyllum is not strongly supported by this study; instead a placement of the genus with Chloranthaceae receives moderate support in the mitochondrial gene analyses. Relationships among magnoliids, monocots, and eudicots remain unresolved. Direct comparisons of analytic results from several data partitions with or without RNA editing sites show that in multigene analyses, RNA editing has no effect on well supported relationships, but minor effect on weakly supported ones. Finally, comparisons of results from separate analyses of mitochondrial and chloroplast genes demonstrate that mitochondrial genes, with overall slower rates of substitution than chloroplast genes, are informative phylogenetic markers, and are particularly suitable for resolving deep relationships.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147147/1/tax25065680.pd

Structure and evolution of the plant cation diffusion facilitator family of ion transporters

Peer reviewedPublisher PD

A Functional Phylogenomic View of the Seed Plants

A novel result of the current research is the development and implementation of a unique functional phylogenomic approach that explores the genomic origins of seed plant diversification. We first use 22,833 sets of orthologs from the nuclear genomes of 101 genera across land plants to reconstruct their phylogenetic relationships. One of the more salient results is the resolution of some enigmatic relationships in seed plant phylogeny, such as the placement of Gnetales as sister to the rest of the gymnosperms. In using this novel phylogenomic approach, we were also able to identify overrepresented functional gene ontology categories in genes that provide positive branch support for major nodes prompting new hypotheses for genes associated with the diversification of angiosperms. For example, RNA interference (RNAi) has played a significant role in the divergence of monocots from other angiosperms, which has experimental support in Arabidopsis and rice. This analysis also implied that the second largest subunit of RNA polymerase IV and V (NRPD2) played a prominent role in the divergence of gymnosperms. This hypothesis is supported by the lack of 24nt siRNA in conifers, the maternal control of small RNA in the seeds of flowering plants, and the emergence of double fertilization in angiosperms. Our approach takes advantage of genomic data to define orthologs, reconstruct relationships, and narrow down candidate genes involved in plant evolution within a phylogenomic view of species' diversification

Climate and air quality impacts due to mitigation of non-methane near-term climate forcers

Over the next few decades, policies that optimally address both climate change and air quality are essential. Although targeting near-term climate forcers (NTCFs), defined here as aerosols, tropospheric ozone and precursor gases (but not methane), should improve air quality, NTCF reductions will also impact climate. How future policies affect the abundance of NTCFs and their impact on climate and air quality remains uncertain. Here, we quantify the 2015–2055 climate and air quality effects of non-methane NTCFs using state-of-the-art chemistry-climate model simulations conducted for the Aerosol and Chemistry Model Intercomparison Project (AerChemMIP). Simulations are driven by two future scenarios featuring similar increases in greenhouse gases (GHGs) but with weak versus strong levels of air quality control measures. Unsurprisingly, we find significant improvements in air quality under NTCF mitigation (strong versus weak air quality controls). Surface ozone (O3) and fine particulate matter (PM2.5) decrease by −15 % and −25 %, respectively, over global land surfaces, with larger reductions in some regions including south and southeast Asia. Non-methane NTCF mitigation, however, leads to additional climate change due to the removal of aerosol which causes a net warming effect, including global mean surface temperature and precipitation increases of 0.24 K and 1.1 %, respectively, with similar increases in extreme weather indices. Regionally, the largest warming and wetting trends occur over Asia, including central and north Asia (0.56 K and 2.1 %), south Asia (0.48 K and 4.6 %) and east Asia (0.44 K and 4.7 %). Relatively large warming and wetting of the Arctic also occurs at 0.41 K and 2.1 %, respectively. Similar surface warming occurs in model simulations with aerosol-only mitigation, implying weak cooling due to ozone reductions. Our findings suggest that future policies that aggressively target non-methane NTCF reductions will improve air quality, but will lead to additional surface warming, particularly in Asia and the Arctic. Policies that address other NTCFs including methane, as well as carbon dioxide emissions, must also be adopted to meet mitigation goals

Conservation of B class gene expression in the second whorl of a basal grass and outgroups links the origin of lodicules and petals

Studies of flower development in core eudicot species have established a central role for B class MADS-box genes in specifying petal and stamen identities. Similarly in maize and rice, B class genes are essential for lodicule and stamen specification, suggesting homology of petals and lodicules and conservation of B class gene activity across angiosperms. However, lodicules are grass-specific organs with a morphology distinct from petals, thus their true homology to eudicot and nongrass monocot floral organs has been a topic of debate. To understand the relationship of lodicules to the sterile floral organs of nongrass monocots we have isolated and observed the expression of B class genes from a basal grass Streptochaeta that diverged before the evolution of lodicules, as well as the outgroups Joinvillea and Elegia, which have a typical monocot floral plan. Our results support a conserved role for B function genes across the angiosperms and provide additional evidence linking the evolution of lodicules and second whorl tepal/petals of monocots. The expression data and morphological analysis suggest that the function of B class genes should be broadly interpreted as required for differentiation of a distinct second floral whorl as opposed to specifying petal identity per se

Evolution of the Telomere-Associated Protein POT1a in \u3cem\u3eArabidopsis thaliana\u3c/em\u3e Is Characterized by Positive Selection to Reinforce Protein-Protein Interaction

Gene duplication is a major driving force in genome evolution. Here, we explore the nature and origin of the POT1 gene duplication in Arabidopsis thaliana. Protection of Telomeres (POT1) is a conserved multifunctional protein that modulates telomerase activity and its engagement with telomeres. Arabidopsis thaliana encodes two divergent POT1 paralogs termed AtPOT1a and AtPOT1b. AtPOT1a positively regulates telomerase activity, whereas AtPOT1b is proposed to negatively regulate telomerase and promote chromosome end protection. Phylogenetic analysis uncovered two independent POT1 duplication events in the plant kingdom, including one at the base of Brassicaceae. Tests for positive selection implemented in PAML revealed that the Brassicaceae POT1a lineage experienced positive selection postduplication and identified three amino acid residues with signatures of positive selection. A sensitive and quantitative genetic complementation assay was developed to assess POT1a function in A. thaliana. The assay showed that AtPOT1a is functionally distinct from single-copy POT1 genes in other plants. Moreover, for two of the sites with a strong signature of positive selection, substitutions that swap the amino acids in AtPOT1a for residues found in AtPOT1b dramatically compromised AtPOT1a function in vivo. In vitro-binding studies demonstrated that all three sites under positive selection specifically enhance the AtPOT1a interaction with CTC1, a core component of the highly conserved CST (CTC1/STN1/TEN1) telomere protein complex. Our results reveal a molecular mechanism for the role of these positively selected sites in AtPOT1a. The data also provide an important empirical example to refine theories of duplicate gene retention, as the outcome of positive selection here appears to be reinforcement of an ancestral function, rather than neofunctionalization. We propose that this outcome may not be unusual when the duplicated protein is a component of a multisubunit complex whose function is in part specified by other members