Nate Upham Profile picture
Evolutionary biologist & Mammalogist @asuSOLS. He/him. Connecting rodent evolution, genomics, & ecology to life's cosmic problems 🌒 \\ Views are my own // #BLM
Oct 19, 2021 10 tweets 11 min read
Glad to share that @ReederLab & I are leading a new NIH R21 project to liberate mammal-to-virus data from publications -- and then annotate them w/ supporting evidence to strengthen spillover risk models

Our approach, newly outlined in @TheLancetPlanet doi.org/10.1016/S2542-…
1/ Image The grant "Intelligently predicting viral spillover risks from bats and other wild mammals" is based from @asuSOLS with co-I @beckettws & team incl @Varsani_lab @taxonbytes @pguptanz w/ @GlobalBiotic & @plazi_ch: reporter.nih.gov/search/qD_Mp36…

Goal: Improve existing host-virus data
2/ Image
Jul 30, 2021 13 tweets 6 min read
Glad to share our work in @CurrentBiology comparing the fossil record & molecular phylogeny for Mammalia over last 100-million yrs.

Phylogeny misses extinctions 66-56 Mya, but is remarkably reliable from 10M to present-day

PDF: authors.elsevier.com/a/1dUcI3QW8Rwp…
doi.org/10.1016/j.cub.…
1/ Image To understand what we found, lets back up to what biologists mean by the "Tree of Life": ancestor-to-descendant relationships reconstructed through time, but also lots of extinction along the way.

As this simulation shows, its really the "Tree of Life & Death" (& taxes!)
2/
Jan 7, 2019 6 tweets 3 min read
Our preprint of Mammalia-wide evolution -- announcing a new tree of life for 5911 species based on a single DNA matrix and fossil node- and tip-dating. We show how ecology (vagility, latitude, diurnality) best explains living diversity & speciation rates. doi.org/10.1101/504803 2/ Bayesian posterior sets of 10,000 trees are built using a 'backbone-and-patch' framework and 31-gene supermatrix of 4098 species (70% of total). This approach gives realistic uncertainty in branch lengths and topology for comparative analyses of mammalian evolutionary rates.