The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.

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One carbon (C1) metabolism plays an important role in marine carbon cycling but the dynamics and modes of C1 transformations are not fully understood. We made contemporaneous measurements of methylamine and methanol metabolism to elucidate the role of C1 compounds as sources of carbon, energy and nitrogen. Methanol and methylamine were predominantly used as an energy source in offshore waters (oxidation rate constant: k : 0.02-0.10 day ; k : 0.01-0.18 day ), but were also important sources of biomass carbon in coastal waters (assimilation rate constant: k : 0.04-0.10 day ; k : 0.01-0.05 day ). The relative extent of assimilation versus oxidation for these substrates correlated positively with chlorophyll, nutrients and heterotrophic bacterial production. Methanol oxidation and assimilation were stimulated significantly by nutrient addition. In contrast, methylamine metabolism was inhibited by ammonium or nitrate, suggesting that methylamine served as a nitrogen source. A preliminary metagenomic survey revealed a diverse population of putative C1-utilizing microorganisms. These results show that the remineralization of methylamine could provide both C and N sources for microbes. Both methanol and methylamine contribute to microbial energetic and carbon substrate demands with a distinctly different signature in nearshore versus offshore environments.

A fundamental problem in landscape ecology is understanding the isolating effects of different patterns of habitat loss and fragmentation on species and ecosystems. In the 21st century, urban development and sea level rise (SLR) are predicted to affect large areas of the United States, further exacerbating already fragmented and densely populated landscapes. Increasing or restoring habitat connectivity may ameliorate these effects, but the broad-reaching efforts required to assess current and future changes to connectivity, especially in low-lying areas vulnerable to SLR, are still under development. To address these issues, we strategically identified a small group of regionally significant species that represent a range of characteristics and ecological requirements useful for examining landscape connectivity. We used expert opinion to parameterize divergent species responses (i.e. resistance) to landscape features and to assess permeability of the landscape. From this, we estimated contemporary and future low-resistance habitat cores in the year 2100. We modeled six species for habitat connectivity using a multiscaled circuit theory-based approach and analysed them collectively to indicate landscape connectivity across the Southeastern United States. Using this approach, we were able to forecast changing connectivity patterns based on predicted urbanization and SLR. Our results suggest that there will be a 41% reduction in the number of low-resistance cores and a 35% decrease in mean area of remaining cores. In addition, current areas of high landscape connectivity will become more fragmented as future connectivity values indicate a more homogenized landscape structure. In the future landscape, pathways for connectivity are likely to move inland and northward as sea level and urbanization pressures increase. Our results may inform more comprehensive planning initiatives regionally or nationally, while simultaneously providing a multiscaled context for localized planning efforts.

Methane is supersaturated in surface seawater and shallow coastal waters dominate global ocean methane emissions to the atmosphere. Aerobic methane oxidation (MOx) can reduce atmospheric evasion, but the magnitude and control of MOx remain poorly understood. Here we investigate methane sources and fates in the East China Sea and map global MOx rates in shallow waters by training machine-learning models. We show methane is produced during methylphosphonate decomposition under phosphate-limiting conditions and sedimentary release is also source of methane. High MOx rates observed in these productive coastal waters are correlated with methanotrophic activity and biomass. By merging the measured MOx rates with methane concentrations and other variables from a global database, we predict MOx rates and estimate that half of methane, amounting to 1.8 ± 2.7 Tg, is consumed annually in near-shore waters (<50 m), suggesting that aerobic methanotrophy is an important sink that significantly constrains global methane emissions.