Genetic insights into population recovery following experimental perturbation in a fragmented landscape

We investigated the mechanism of population recovery in the Australian bush rat, Rattus fuscipes, following experimental perturbation in a fragmented landscape. Our study involved genetic monitoring over 24 months following the removal of animals from seven sites by intense trapping. A total of 171 bush rats was removed and statistical analysis confirmed a significant knockdown. At one site, local extinction followed the perturbation, while population sizes at 24 months varied from 37% to 90% of the original population size at the remaining sites. The outcomes of genetic analysis at 11 microsatellite loci and mtDNA indicated that population recovery was achieved predominantly by residual animals: recovery populations were genetically more similar to their respective pre-treatment population than near neighbours; assignment tests detected few immigrants; there was no influx of new immigrant alleles and haplotypes. This finding is consistent with emerging evidence for restricted gene flow in bush rats. The local extinction observed at one site indicate that, under severe perturbation restricted dispersal limits opportunities for, and the rate of, population recovery. Thus, while the bush rat appears resilient to substantial population size perturbation, once a critical minimum population size threshold has been reached, this species may be susceptible to local extinction. We concluded that some widespread species currently predicted to be extinction-resilient may, in fact, be at risk if localized extinctions occur and dispersal limitations prevent recolonisation.     

The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome

We have sequenced and annotated the genome of the filamentous ascomycete Ashbya gossypii. With a size of only 9.2 megabases, encoding 4718 protein-coding genes, it is the smallest genome of a free-living eukaryote yet characterized. More than 90% of A. gossypii genes show both homology and a particular pattern of synteny with Saccharomyces cerevisiae. Analysis of this pattern revealed 300 inversions and translocations that have occurred since divergence of these two species. It also provided compelling evidence that the evolution of S. cerevisiae included a whole genome duplication or fusion of two related species and showed, through inferred ancient gene orders, which of the duplicated genes lost one copy and which retained both copies.     

Dissection of a major QTL for seed colour and fibre content in Brassica napus reveals colocalization with candidate genes for phenylpropanoid biosynthesis and flavonoid deposition

A major quantitative trait locus (QTL) influencing seed fibre and colour in Brassica napus was dissected by marker saturation in a doubled haploid (DH) population from the black‐seeded oilseed rape line ‘Express 617’ crossed with a yellow‐seeded B. napus line, ‘1012–98’. The marker at the peak of a sub‐QTL with a strong effect on both seed colour and acid detergent lignin content lay only 4 kb away from a Brassica (H+)‐ATPase gene orthologous to the transparent testa gene AHA10. Near the peak of a second sub‐QTL, we mapped a copy of the key phenylpropanoid biosynthesis gene cinnamyl alcohol dehydrogenase, while another key phenylpropanoid biosynthesis gene, cinnamoyl co‐a reductase 1, was found nearby. In a cross between ‘Express 617’ and another dark‐seeded parent, ‘V8’, Bna.CCR1 was localized in silico near the peak of a corresponding seed fibre QTL, whereas in this case Bna.CAD2/CAD3 lay nearby. Re‐sequencing of the two phenylpropanoid genes via next‐generation amplicon sequencing revealed intragenic rearrangements and functionally relevant allelic variation in the three parents.