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The Arctic climate is changing. Permafrost is warming, hydrological processes are changing and biological and social systems are also evolving in response to these changing conditions. Knowing how the structure and function of arctic terrestrial ecosystems are responding to recent and persistent climate change is paramount to understanding the future state of the Earth system and how humans will need to adapt. Our holistic review presents a broad array of evidence that illustrates convincingly; the Arctic is undergoing a system-wide response to an altered climatic state. New extreme and seasonal surface climatic conditions are being experienced, a range of biophysical states and processes influenced by the threshold and phase change of freezing point are being altered, hydrological and biogeochemical cycles are shifting, and more regularly human sub-systems are being affected. Importantly, the patterns, magnitude and mechanisms of change have sometimes been unpredictable or difficult to isolate due to compounding factors. In almost every discipline represented, we show Climatic Change (2005) 72: 251-298 how the biocomplexity of the Arctic system has highlighted and challenged a paucity of integrated scientific knowledge, the lack of sustained observational and experimental time series, and the technical and logistic constraints of researching the Arctic environment. This study supports ongoing efforts to strengthen the interdisciplinarity of arctic system science and improve the coupling of large scale experimental manipulation with sustained time series observations by incorporating and integrating novel technologies, remote sensing and modeling.

Diet and host phylogeny drive the taxonomic and functional contents of the gut microbiome in mammals, yet it is unknown whether these patterns hold across all vertebrate lineages. Here, we assessed gut microbiomes from ∼900 vertebrate species, including 315 mammals and 491 birds, assessing contributions of diet, phylogeny, and physiology to structuring gut microbiomes. In most nonflying mammals, strong correlations exist between microbial community similarity, host diet, and host phylogenetic distance up to the host order level. In birds, by contrast, gut microbiomes are only very weakly correlated to diet or host phylogeny. Furthermore, while most microbes resident in mammalian guts are present in only a restricted taxonomic range of hosts, most microbes recovered from birds show little evidence of host specificity. Notably, among the mammals, bats host especially bird-like gut microbiomes, with little evidence for correlation to host diet or phylogeny. This suggests that host-gut microbiome phylosymbiosis depends on factors convergently absent in birds and bats, potentially associated with physiological adaptations to flight. Our findings expose major variations in the behavior of these important symbioses in endothermic vertebrates and may signal fundamental evolutionary shifts in the cost/benefit framework of the gut microbiome. IMPORTANCE In this comprehensive survey of microbiomes of >900 species, including 315 mammals and 491 birds, we find a striking convergence of the microbiomes of birds and animals that fly. In nonflying mammals, diet and short-term evolutionary relatedness drive the microbiome, and many microbial species are specific to a particular kind of mammal, but flying mammals and birds break this pattern with many microbes shared across different species, with little correlation either with diet or with relatedness of the hosts. This finding suggests that adaptation to flight breaks long-held relationships between hosts and their microbes.

The move from OTU-based to sOTU-based analysis, while providing additional resolution, also introduces computational challenges. We demonstrate that one popular method of dealing with sOTUs (building a de novo tree from the short sequences) can provide incorrect results in human gut metagenomic studies and show that phylogenetic placement of the new sequences with SEPP resolves this problem while also yielding other benefits over existing methods.

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