Articles

A combination of analysis of plasmid diversity in the gut of hospitalized patients with experimental evolution shows that the evolution of plasmid-mediated antibiotic resistance involves a trade-off between antibiotic resistance levels and bacterial fitness.

Analysis of a dataset of the morphology of more than 250,000 adult birds of 105 species over a 30 year period across North America reveals changes in body size and relative wing length over time and with relation to latitude, elevation and temperature variation.

Multiple factors contribute to the independent evolution of the same adaptations in nature. This study quantifies parallel evolution among species of Timema stick insects and shows that the degree of parallelism is determined by shared ecology and genomic background.

The authors report genetic, archaeological and stable isotopic data from two late Palaeolithic individuals in Britain, from Gough's Cave and Kendrick's Cave. The individuals differ not only in their ancestry but also their diets, ecologies and mortuary practices, revealing diverse origins and lifeways among inhabitants of late Pleistocene Britain.

Analysis of genomes in a phylogenetic context reveals a 350-million-year-old homomorphic sex chromosome in molluscs, probably maintained by regulation of reversible sex-biased genes and sex chromosome turnover.

Analysis of the DNA methylomes of two ecomorphs of Astatotilapia calliptera from a single lake, which diverged about 1,000 years ago plus a third riverine ecomorph, from which they likely separated about 10,000 years ago, shows epigenetic differences associated with altered transcriptional activity of ecologically relevant genes, despite low levels of genetic divergence.

Analysis of genomes, epigenomes and transcriptomes of developing sea urchins with divergent life histories shows how natural selection can reshape developmental gene regulatory networks.

Comparing global vegetation trait patterns derived from citizen science data versus those from scientific survey plots, the authors reveal high correlations between the two approaches and improvements over previously published trait maps.

The identification of 21 large inversion polymorphisms in populations of deer mice shows that they are widespread, important for patterns of recombination and likely to be involved in local adaptation.

Compiling data on floral introductions and European colonial history of regions worldwide, the authors find that compositional similarity of floras is higher than expected among regions once occupied by the same empire and similarity increases with the length of time the region was occupied by that empire.

A theoretical model of a community of species under selection for compatibility between nuclear and mitochondrial genomes predicts patterns of species diversity, abundance, speciation and extinction, and also suggests a link between metabolic demands and latitudinal variation in diversity.

Analysing a compilation of planktonic foraminifera assemblage time series covering the past 24,000 years, from the last ice age to the current warm period, the authors find that responses to warming were highly heterogeneous leading to the emergence of novel assemblages and possibly new ecological interactions.

In the Sahel region of West Africa, An. coluzzii mosquitoes appear to survive the dry season locally, but the relative contribution of this subpopulation to the persistence of the species in the Sahel has remained unknown. Here the authors use stable isotope tracking to determine the fraction of mosquitoes that undergo aestivation, a state of dormancy that allows them to persist through the dry season and maintain yearly malaria transmission.

Analysing a long-term tracking dataset of migrating mule deer, the authors show that the expansion of natural gas energy infrastructure over 14 years along a migratory corridor changes deer behaviour and reduces by more than 38% their ability to keep pace with spring vegetation green-up.

There are many open questions about biogeochemical function in peatlands. Here, the authors investigate the nitrogen cycle of tropical peatlands, finding that a surprisingly high fraction of nitrous oxide production is abiotic and that denitrification is a coupled abiotic-biotic process.

Using individual transcriptomes of two ant species, the authors show that caste differentiation is canalized from early development and identify key regulatory genes for the development of ant caste phenotypes.

A comparison of fish community data with reef coral and macroalgae cover at several sites around Polynesia over 11 years and spanning disturbance events suggests that fish community diversity has only minimal influence on coral dynamics, including recovery from disturbance.

Quantifying changing climatic effects on ecosystem productivity and human spatiotemporal distributions during the Middle to Upper Palaeolithic transition in Iberia, the authors find evidence that the hiatus between Neanderthal and modern human cultural complexes in North Atlantic Iberia and the longer persistence of Neanderthals in southern latitudes had an ecological cause.

Fossil calibrations, a relative clade age calibration (informed by horizontal gene transfer) and new phylogenomic methods for mapping gene family origins resolve tracheophytes (vascular plants) and bryophytes (non-vascular plants) as monophyletic sister groups that diverged during the Cambrian, 515–494 million years ago. The early evolution of both groups, but particularly that of bryophytes, was characterized by major gene content change.

In realistic high-dimensional fitness landscapes of RNA secondary structure, protein tertiary structure and protein complexes, fitness peaks can be easily reached from any starting point without traversing fitness valleys.