The Mammalian Ecology and Conservation Unit has dedicated significant energy over the past 5 years towards developing and utilizing next generation sequencing tools on a variety topics related to the ecology, evolution, and conservation of mammals and other vertebrates. Below are some of the current next generation sequencing-based project in progress at the MECU:
WHOLE GENOME SEQUENCING, ASSEMBLY, AND RESEQUENCING
- Whole genome sequencing and assembly of the mule deer via Hi-C, 10X Genomics, and PacBio; primary investigators: Mike Buchalski (Cal Dept Fish Wildl), Daphne Gille (Cal Dept Fish Wildl), Ben Sacks (UCD MECU)
- Draft genome assembly of the tule elk and 5x resequencing of Roosevelt and Rocky Mountain elk using HiSeq3000/4000 PE 150; primary investigators: Jessica Mizzi (UCD), Titus Brown (UCD), Erin Meredith (Cal Dept Fish Wildl), Zach Lounsberry (UCD MECU), Ben Sacks (UCD MECU)
- Himalayan and Indian wolf 5x resequencing; primary investigators: Lauren Hennelly (UCD MECU), Ben Sacks (UCD MECU), Bilal Habib (Wildlife Institute of India), Shrushti Modi (Wildlife Institute of India)
TARGET CAPTURE ENRICHMENT SEQUENCING
- Y chromosome phylogenetics of wolflike canids and foxes; Ben Sacks (UCD MECU), Zach Lounsberry (UCD MECU), Mark Statham (UCD MECU), Steve Fain (USFWS, National Forensics Lab)
- Ancient mtDNA from dogs across the arctic (see Mitogenome sequencing below); primary investigators: Sarah Brown (UCD MECU), Christyann Darwent (UCD Anthro), Ben Sacks (UCD MECU)
- Immune-gene capture in dogs, foxes, and wolflike canines; primary investigators: Niels Pedersen (UCD), Hongwei Liu (UCD), Zach Lounsberry (UCD MECU), Ben Sacks (UCD MECU)
MITOGENOME SEQUENCING AND ASSEMBLY
- North Pacific albatrosses; primary investigators: Zach Lounsberry (UCD MECU), Ben Sacks (UCD MECU), Sarah Brown (UCD MECU), Paul Collins