Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

/pdf/comparative-genomics-reveals-insights-into-avian-genome-3gamkx0zqj.pdf

Comparative genomics reveals insights into avian genome evolution and adaptation.

Aim To review published evidence regarding the factors that influence the geographic variation in diversity of soil organisms at different spatial scales.

Location  Global.

Methods  A search of the relevant literature was conducted using the Web of Science and the author's personal scientific database as the major sources. Special attention was paid to include seminal studies, highly cited papers and/or studies highlighting novel results.

Results  Despite their significant contribution to global biodiversity, our taxonomic knowledge of soil biota is still poor compared with that of most above-ground organisms. This is particularly evident for small-bodied taxa. Global patterns of soil biodiversity distribution have been poorly documented and are thought to differ significantly from what is reported above-ground. Based on existing data, it appears that microorganisms do not respond to large-scale environmental gradients in the same way as metazoans. Whereas soil microflora seem to be mainly represented by cosmopolitan species, soil animals respond to altitudinal, latitudinal or area gradients in the same way as described for above-ground organisms. At local scales, there is less evidence that local factors regulate above- and below-ground communities in the same way. Except for a few taxa, the humpbacked response to stress and disturbance gradients doesn't seem to apply underground. Soil communities thus appear weakly structured by competition, although competitive constraints may account for assembly rules within specific taxa. The main factor constraining local soil biodiversity is the compact and heterogeneous nature of soils, which provides unrivalled potential for niche partitioning, thus allowing high levels of local biodiversity. This heterogeneity is increased by the impact of ecosystem engineers that generate resource patchiness at a range of spatio-temporal scales.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1466-8238.2009.00517.x

Macroecological patterns in soil communities

Terrestrial ecologists and soil modelers have traditionally portrayed the inhabitants of soil as a black box labeled as "soil fauna" or "decomposers or detritivores” assuming that they just merely recycle the deposited dead plant material. Soil is one of the most diverse habitats on Earth and contains one of the most diverse assemblages of living organisms; however, the opacity of this world has severely limited our understanding of their functional contributions to soil processes and to ecosystem resilience. Traditional taxonomy, based on morphological and anatomical aspects, is becoming replaced by rapid processing molecular techniques (e.g. with marker gene-based approaches). However, this may be impracticable in many ecological studies and consequently, the majority of the current knowledge, still contributes little to our understanding of their role in ecosystem functioning. Over the years, different workers have produced several ‘functional classifications’ based on the body width, feeding regime, certain behavioral and reproductive aspects and ecological niches of soil organisms. Unfortunately, the information available is severely restricted to ‘major’ groups. A better physiological and metabolic understanding of when and how a complex community of soil organisms access nutrients, alter their environment and in turn, affect soil processes, will allow a more realistic quantitative evaluation of their ecological roles in the biogeochemical cycles. Here, I review the applicability of the available approaches, highlight future research challenges and propose a dynamic conceptual framework that could improve our ability to solve this functional puzzle.

/pdf/soil-fauna-and-soil-functions-a-jigsaw-puzzle-37vgf0bp71.pdf

Soil fauna and soil functions: a jigsaw puzzle

High-throughput DNA methods hold great promise for the study of taxonomically intractable mesofauna of the soil. Here, we assess species diversity and community structure in a phylogenetic framework, by sequencing total DNA from bulk specimen samples and assembly of mitochondrial genomes. The combination of mitochondrial metagenomics and DNA barcode sequencing of 1494 specimens in 69 soil samples from three geographic regions in southern Iberia revealed >300 species of soil Coleoptera (beetles) from a broad spectrum of phylogenetic lineages. A set of 214 mitochondrial sequences longer than 3000 bp was generated and used to estimate a well-supported phylogenetic tree of the order Coleoptera. Shorter sequences, including cox1 barcodes, were placed on this mitogenomic tree. Raw Illumina reads were mapped against all available sequences to test for species present in local samples. This approach simultaneously established the species richness, phylogenetic composition and community turnover at species and phylogenetic levels. We find a strong signature of vertical structuring in soil fauna that shows high local community differentiation between deep soil and superficial horizons at phylogenetic levels. Within the two vertical layers, turnover among regions was primarily at the tip (species) level and was stronger in the deep soil than leaf litter communities, pointing to layer-mediated drivers determining species diversification, spatial structure and evolutionary assembly of soil communities. This integrated phylogenetic framework opens the application of phylogenetic community ecology to the mesofauna of the soil, among the most diverse and least well-understood ecosystems, and will propel both theoretical and applied soil science.

/pdf/phylogenetic-community-ecology-of-soil-biodiversity-using-40kyo4dy0u.pdf

Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics

Soil nematodes are a foremost component of terrestrial biodiversity; they display a whole gamut of trophic guilds and life strategies, and by their activity, affect major ecosystem process, such as organic matter degradation and carbon cycling. Based on nematodes' functional types, nematode community indices have been developed, and can be used to link variation in nematodes community composition and ecosystem processes. Yet, the use of these indices has been mainly restricted to anthropogenic stresses. In this study, we propose to expand the use of nematodes' derived ecological indices to link soil and climate properties with soil food webs, and ecosystem processes that all vary along steep elevation gradients. For this purpose, we explored how elevation affects the trophic and functional diversity of nematode communities sampled every 300 m, from about 1,000 m to 3,700 m above sea level, across four transects in the lesser Himalayan range of Jammu and Kashmir. We found that (a) the trophic and functional diversity of nematodes increases with elevation; (b) differences in nematodes communities generate habitat-specific functional diversity; (c) the maturity index (ΣMI) increases with elevation, while the enrichment index decreases, indicating less mature and less productive ecosystems, enhanced fungal-based energy flow, and a predominant role of nematodes in generating carbon influxes at high-elevation sites. We thus confirm that the functional contribution of soil nematodes to belowground ecosystem processes, including carbon and energy flow, is stronger at high elevation. Overall, this study highlights the central importance of nematodes in sustaining soil ecosystems and brings insights into their functional role, particularly in alpine and arctic soils.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.8061

The functional role and diversity of soil nematodes are stronger at high elevation in the lesser Himalayan Mountain ranges.

Soils are recognized as one of the greatest biodiversity reservoirs of the planet, as communities of edaphic animals include an outstanding diversity of body sizes, life forms and behaviours, with representatives of virtually all the major taxa and trophic groups that form the terrestrial animal kingdom. Paradoxically, soils are also among the most poorly studied habitats of our planet, and we most likely only know an infinitesimal part of the global taxonomic and functional diversity of its biota. In this paper, we provide a ‘state-of-the-art’ review and reveal the main gaps in our knowledge of soil animal diversity, its function and how it contributes to the provision of important ecosystem services. We also propose some further research priorities for improving our knowledge of soil fauna and contributing to a better conservation of their communities.

Priorities for conservation of soil animals

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Priorities for conservation of soil animals