Tables and Figures
Figure 1 Overview of sequenced species and reference genome assemblies generated in this study . (a) Photographs of the five marsupial species sequenced. A yellow-footed antechinus (Antechinus flavipes ), silver-headed antechinus (Antechinus argentus ), and black-tailed dusky antechinus (Antechinus arktos ) from Australia; a black-tailed dasyure (Murexia melanurus ) from Papua New Guinea. Antechinus spp. and M. melanurusphotographs are courtesy of A.M. Baker and John Hornbuckle, respectively. (b) Circos plot of the reference genome assembly ofA. flavipes . The outermost segment represents chromosome sequences, with the numbers on the external surface indicating genome size in Mb. Chr7 in A. flavipes corresponds to the X chromosome. The line plots, from outside to inside represent the distribution of CDS density (from 0 to 0.15), GC content (from 0.30 to 0.65) and TE ratio (from 0.2 to 1.0). Frequencies were calculated in 500-kb sliding windows. (c) Circos plot showing shared synteny of Antechinus flavipes (chr1-chr7) and Sarcophilus harrisii(NC_045426.1-NC_045432.1). Aligned using LASTZ. The synteny blocks are linked using lines coloured in accordance with the A. flavipeschromosomes. Aligned blocks with length shorter than 20 kb are not shown. Chr7 in A. flavipes corresponds to the X chromosome ofSarcophilus harrisii .
Figure 2 Evolutionary history of semelparous mammals. (a) Inferred phylogeny of ten marsupials and the platypus (outgroup) based on fourfold degenerate sites from 6,431 1:1 orthologs. Blue numbers at nodes represent the estimated divergence time from present (million years ago; Mya) between lineages. Semelparous lineages are indicated in red. (b) Demography of the dasyurid subfamily Phascogalinae. Historic population sizes (Ne ) were estimated using the pairwise sequentially Markovian coalescent (PSMC) method (Li & Durbin, 2011) and diploid genome sequences. The x -axis shows the time before present in years on a log scale; the dashed gray line shows human arrival in Australia 59.3 to 65 kya (Clarkson et al., 2017); red dots indicate the extinction times of 15 species of Pleistocene Sahul (Saltre et al., 2016). The y -axis showsNe , with bootstrap estimates indicated by lighter lines. Plots were scaled using a mutation rate (μ ) of 1.37 × 10-9 substitutions nucleotide-1 generation-1 and species-specific generation times (g ) of one year. Two A. flavipes individuals were interrogated (coloured in orange and blue). (c) Map showing the location (coloured circles) and elevation (mamsl; metres above sea level) of sampled dasyurids (see subfigure b).
Figure 3 Gene expression profiling of the Antechinus flavipes breeding cycle. (a) Schematic overview of the yellow-footed antechinus (Antechinus flavipes ) breeding season in Samford Valley, Queensland, Australia. Free-CORT illustrates an increase in the level of free (unbound) stress hormones (chiefly the corticosteroid cortisol) in males during the breeding season of antechinuses (based on three studies illustrated in (Naylor et al., 2008)). (b) Rapid organismal senescence of male A. flavipes . Left, male (~11 months of age) prior to the breeding season. Right, late breeding stage male (~11.5 months of age). Note the loss of fur clumps and deterioration of body condition. (c) In the moribund state, when other energy stores have been depleted, skeletal muscle catabolism generates amino acids for gluconeogenesis, induced by the corticosteroid, cortisol. (d) Venn diagram for the overlap of significantly up-regulated (left) or down-regulated (right) genes in moribund male antechinuses. Called by limma v3.22.1 (≥1.5-fold change and P ≤0.01). (e) Heat map of selected energy metabolism genes differentially expressed in the skeletal muscle of moribund male antechinuses. Moribund samples are indicated by a red bar below the map. Scaled TMM-normalised read counts (denoted as the row Z score) are plotted, with red indicating high expression and blue indicating low expression. BPGM , 2,3-bisphosphoglycerate mutase; FBP2 , fructose-bisphosphatase 2; GPI , glucose-6-phosphate isomerase;LDHA , lactate dehydrogenase A; PFKM , phosphofructokinase, muscle; PGK2 , phosphoglycerate kinase 2; PKM , pyruvate kinase M1/2; GPD1 , glycerol-3-phosphate dehydrogenase 1;GPD2 , glycerol-3-phosphate dehydrogenase 2; SLC2A5 , solute carrier family 2 member 5; SLC37A4 , solute carrier family 37 member 4; PRKAG3 , protein kinase AMP-activated non-catalytic subunit gamma 3; STK11 , serine/threonine kinase 11. (f) Expression pattern of the AMPK regulator LKB1 (STK11 ) in male (left) and female (right) tissues throughout the breeding season. Counts per million TMM-normalized counts, with standard error bars.
Table 1. Antechinus flavipes genome assembly statistics