Joseph Guhlin, Marissa F Le Lec, Jana Wold, Emily Koot, David Winter, Patrick J Biggs, Stephanie J Galla, Lara Urban, Yasmin Foster, Murray P Cox, Andrew Digby, Lydia R Uddstrom, Daryl Eason, Deidre Vercoe, Tāne Davis, Jason T Howard, Erich D Jarvis, Fiona E Robertson, Bruce C Robertson, Neil J Gemmell, Tammy E Steeves, Anna W Santure, Peter K Dearden
The kākāpō is a critically endangered, intensively managed, long-lived nocturnal parrot endemic to Aotearoa New Zealand. We generated and analysed whole-genome sequence data for nearly all individuals living in early 2018 (169 individuals) to generate a high-quality species-wide genetic variant callset. We leverage extensive long-term metadata to quantify genome-wide diversity of the species over time and present new approaches using probabilistic programming, combined with a phenotype dataset spanning five decades, to disentangle phenotypic variance into environmental and genetic effects while quantifying uncertainty in small populations...
August 28, 2023: Nature Ecology & Evolution