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I'm spending the week at the American Museum of Natural History to participate in a week-long workshop learning about all things ancient DNA analysis! The workshop, jointly hosted by AMNH and the Center for Evolutionary Hologenomics, University of Copenhagen, aims to teach us about bioinformatics pipelines and genomics approaches for aDNA and highly degraded hDNA analysis.
Day 1 - Intro to aDNA analysis
Day 2 - Ancient Wolf vs Dog Challenge
We undertook a fun challenge to figure out if a "mystery sample" from northern Russia is more closely related to modern dogs or ancient wolves. My group had a mystery sample that clustered much more closely with ancient wolves, and in particular the Ulakhan Sular ancient wolves (see my ADMIXTURE plot below). The frozen canine, which shared morphological characteristics with both wolves and early dogs, was presumed to be an early ancestor to all modern dogs.
Day 3 - Night at the Museum!
After a full day of learning about phylogenetic inference, we had some time to explore the museum after-hours. The AMNH even re-tweeted me!
Day 4 - F-statistics and PCA
We dove deeper on our Ancient "wolf" sample from Day 2 and used F-stats and PCA to better understand how it relates to ancient wolves and modern dogs. See my results below!
Day 5 - aDNA for Conservation Genomics
I was very excited that the last topic of the workshop was using aDNA for conservation, which relates to many of my research interests. We used a dataset of contemporary and historic (pre-1960s) African rhinos in order to determine if their populations were undergoing genomic erosion and loss of heterozygosity with population decline from sport hunting. Here are the results ...
Interestingly, the results (heterozygosity and runs of homozygosity) don't show overwhelming evidence for genomic erosion. As breeding populations become increasingly fractured, these measures may shift over time. This data is from the U. of Copenhagen, credit to Dr. Claudia Fontsere.
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