Adaptation and conservation insights from the koala genome

Abstract

The koala, the only extant species of the marsupial family Phascolarctidae, is classified as 'vulnerable' due to habitat loss and widespread disease. We sequenced the koala genome, producing a complete and contiguous marsupial reference genome, including centromeres. We reveal that the koala's ability to detoxify eucalypt foliage may be due to expansions within a cytochrome P450 gene family, and its ability to smell, taste and moderate ingestion of plant secondary metabolites may be due to expansions in the vomeronasal and taste receptors. We characterized novel lactation proteins that protect young in the pouch and annotated immune genes important for response to chlamydial disease. Historical demography showed a substantial population crash coincident with the decline of Australian megafauna, while contemporary populations had biogeographic boundaries and increased inbreeding in populations affected by historic translocations. We identified genetically diverse populations that require habitat corridors and instituting of translocation programs to aid the koala's survival in the wild.

A practical introduction to sequentially Markovian coalescent methods for estimating demographic history from genomic data

“…In principle, one can reconstruct the demographic history of a species from the genome sequences of its present‐day representatives (Beichman, Huerta‐Sanchez, & Lohmueller, ). These reconstructions can be used to answer various biological questions, such as the influence of climatic events on population size and structure (Miller et al, ), the timing of major events in the evolutionary history of modern humans (Fu et al, ; Li & Durbin, ), human impacts on wild animal populations (Johnson et al, ; Pujolar, Dalén, Hansen, & Madsen, ), and the effects of domestication (Frantz et al, ; Yu et al, ).…”

Non-linear sequence similarity between the Xist and Rsx long noncoding RNAs suggests shared functions of tandem repeat domains

“…In contrast to Xist, which is mostly comprised of non-repetitive sequence, nearly all of the sequence in Rsx can be assigned to one of four repetitive domains ( Figure 1D; (Johnson et al, 2018)). Here, we refer to the repetitive domains in Rsx as Repeats 1 through 4.…”

“…However, because of the conservation of Repeat D-like domains in non-murid eutherian mammals ( Figure S1; (Nesterova et al, 2001;Yen et al, 2007)), we also included the sequence of human Xist Repeat D in our analyses. We used the sequence from koala Rsx as our exemplar, owing to the high-quality of the koala genome build relative to builds from other marsupials (Johnson et al, 2018).…”

Genetic Management of Captive and Reintroduced Bilby Populations

“…Researchers are now able to identify large numbers of hypervariable genetic markers, such as single nucleotide polymorphisms (SNPs), which can often be linked to specific genes or genome regions of interest (Morin et al , Wright et al ). The availability of whole genome sequence data from non‐model species is facilitating the exploration of population structure, life history, and behavioral and reproductive strategies in a range of threatened fauna (Allendorf et al , Eldridge , Johnson et al ). Despite the growing number of population and conservation genetics studies in the literature, routine genetic monitoring using hypervariable markers has yet to be widely integrated into ongoing threatened species recovery efforts (Frankham , Shafer et al ).…”