Environment–host–microbial interactions shape the Sarraceniapurpurea microbiome at the continental scale

The importance of climate, habitat structure, and higher trophic levels on microbial diversity is only beginning to be understood. Here, we examined the influence of climate variables, plant morphology, and the abundance of aquatic invertebrates on the microbial biodiversity of the northern pitcher plant Sarracenia purpurea. The plant\u27s cup‐shaped leaves fill with rainwater and support a miniature, yet full‐fledged, ecosystem with a diverse microbiome that decomposes captured prey and a small network of shredding and filter‐feeding aquatic invertebrates that feed on microbes. We characterized pitcher microbiomes of 108 plants sampled at 36 sites from Florida to Quebec. Structural equation models revealed that annual precipitation and temperature, plant size, and midge abundance had direct effects on microbiome taxonomic and phylogenetic diversity. Climate variables also exerted indirect effects through plant size and midge abundance. Further, spatial structure and climate influenced taxonomic composition, but not phylogenetic composition. Our results suggest that direct effects of midge abundance and climate and indirect effects of climate through its effect on plant‐associated factors lead to greater richness of microbial phylotypes in warmer, wetter sites

For common community phylogenetic analyses, go ahead and use synthesis phylogenies

Should we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose‐built phylogeny) requires more effort, expertise, and cost than subsetting an already available phylogeny (synthesis‐based phylogeny). However, we still lack a comparison of how these two approaches to building phylogenetic trees influence common community phylogenetic analyses such as comparing community phylogenetic diversity and estimating trait phylogenetic signal. Here, we generated three purpose‐built phylogenies and their corresponding synthesis‐based trees (two from Phylomatic and one from the Open Tree of Life, OTL). We simulated 1,000 communities and 12,000 continuous traits along each purpose‐built phylogeny. We then compared the effects of different trees on estimates of phylogenetic diversity (alpha and beta) and phylogenetic signal (Pagel’s λ and Blomberg’s K). Synthesis‐based phylogenies generally yielded higher estimates of phylogenetic diversity when compared to purpose‐built phylogenies. However, resulting measures of phylogenetic diversity from both types of phylogenies were highly correlated (Spearman’s ρ > 0.8 in most cases). Mean pairwise distance (both alpha and beta) is the index that is most robust to the differences in tree construction that we tested. Measures of phylogenetic diversity based on the OTL showed the highest correlation with measures based on the purpose‐built phylogenies. Trait phylogenetic signal estimated with synthesis‐based phylogenies, especially from the OTL, was also highly correlated with estimates of Blomberg’s K or close to Pagel’s λ from purpose‐built phylogenies when traits were simulated under Brownian motion. For commonly employed community phylogenetic analyses, our results justify taking advantage of recently developed and continuously improving synthesis trees, especially the Open Tree of Life.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151322/1/ecy2788_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151322/2/ecy2788.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151322/3/ecy2788-sup-0001-AppendixS1.pd

Ecogeographical rules and the macroecology of food webs

AimHow do factors such as space, time, climate and other ecological drivers influence food web structure and dynamics? Collections of well‐studied food webs and replicate food webs from the same system that span biogeographical and ecological gradients now enable detailed, quantitative investigation of such questions and help integrate food web ecology and macroecology. Here, we integrate macroecology and food web ecology by focusing on how ecogeographical rules [the latitudinal diversity gradient (LDG), Bergmann’s rule, the island rule and Rapoport’s rule] are associated with the architecture of food webs.LocationGlobal.Time periodCurrent.Major taxa studiedAll taxa.MethodsWe discuss the implications of each ecogeographical rule for food webs, present predictions for how food web structure will vary with each rule, assess empirical support where available, and discuss how food webs may influence ecogeographical rules. Finally, we recommend systems and approaches for further advancing this research agenda.ResultsWe derived testable predictions for some ecogeographical rules (e.g. LDG, Rapoport’s rule), while for others (e.g., Bergmann’s and island rules) it is less clear how we would expect food webs to change over macroecological scales. Based on the LDG, we found weak support for both positive and negative relationships between food chain length and latitude and for increased generality and linkage density at higher latitudes. Based on Rapoport’s rule, we found support for the prediction that species turnover in food webs is inversely related to latitude.Main conclusionsThe macroecology of food webs goes beyond traditional approaches to biodiversity at macroecological scales by focusing on trophic interactions among species. The collection of food web data for different types of ecosystems across biogeographical gradients is key to advance this research agenda. Further, considering food web interactions as a selection pressure that drives or disrupts ecogeographical rules has the potential to address both mechanisms of and deviations from these macroecological relationships. For these reasons, further integration of macroecology and food webs will help ecologists better understand the assembly, maintenance and change of ecosystems across space and time.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151318/1/geb12925_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151318/2/geb12925.pd

SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues

Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types

SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues

Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types

A first update on mapping the human genetic architecture of COVID-19

peer reviewe

Functional and phylogenetic diversity of sharks in the northeastern Pacific

Data associated with the trait compilation and phylogenetic reconstruction for sharks of the northeastern Pacifi

Pine Rockland Community Phylogeny

This file is a maximum clade credibility (MCC) phylogeny resulting from a BEAST analysis of 540 pine rockland plant taxa in nexus (.nex) format