Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation

Salmonella enterica serotype Typhimurium (S. Typhimurium) is a leading cause of gastroenteritis and disseminated disease worldwide. Two S. Typhimurium strains (SL1344 and ATCC14028) are widely used to study host-pathogen interactions, yet genotypic variation results in strains with diverse host range, pathogenicity and risk to food safety. A robust fully parsimonious phylogenetic tree constructed from recombination purged variation in the whole genome sequence of 131 diverse strains of S. Typhimurium revealed population structure composed of two high order clades (α and β) and multiple subclades on extended internal branches, that exhibited distinct signatures of host adaptation and anthropogenic selection. Clade α contained a number of subclades composed of strains from well characterized epidemics in domesticated animals, while clade β predominantly contained subclades associated with wild avian species, with the notable exception of a subclade containing the DT204/49 complex. The contrasting epidemiology of α and β strains was reflected in a distinct distribution of antimicrobial resistance (AMR) genes, accumulation of hypothetically disrupted coding sequences (HDCS), and signatures of functional diversification associated with invasiveness of host adapted serotypes. Gene flux was predominantly driven by acquisition, loss or recombination of prophage. The acquisition of large genetic islands (SGI-1 and 4) was limited to two recent pandemic clones (DT104 and monophasic S. Typhimurium ST34) in clade α. Together, our data are consistent with the view that a broad host range common ancestor of S. Typhimurium diversified with clade α lineages remained largely associated with multiple domesticated animal species, while clade β spawned multiple lineages that underwent diversifying selection associated with adaptation to various niches, predominantly in wild avian species.

Much Ado about Mutton

This chapter examines the fraught attempts to acclimatize Spanish merino sheep in Britain in the early nineteenth century. Proponents of the merino were motivated by the commercial value of merino wool, which is and was exceptionally fine, but the debate over the merino’s place in Britain ultimately came down to its flesh. The breed’s opponents argued that merino mutton was inferior to that of British breeds like the New Leicester, and further that the fineness of merino wool was dependent upon Spain’s climate and environment. The long and acrimonious controversy which attended the merino’s attempted naturalization in Great Britain revealed the degree to which competing understandings of the relative influence of climate or environment and anthropogenic selection in sheep-breeding unsettled the very category of breed itself. Ultimately, attempts to acclimatize merino sheep in Britain failed, as its wool (although finer than that of “native” British breeds) grew coarser under Britain’s damper climate, and its leaner carcass offended the proud palates of British diners.

A Breed in Any Other Place

This chapter explores “native” British breeds within the context of agricultural improvement at the turn of the nineteenth century, arguing that the idea of a native breed arose at the same time and in opposition to that of an “improved” breed. Breeds were understood to encompass the relationship between heredity, anthropogenic selection, and the influence of climate or environment, although which of these factors was understood to take precedence could and did vary. As breeders increasingly selected their animals for early maturity, meatiness, or particular kinds of wool in the case of sheep in conformation with market imperatives, “native” came to signal a type of livestock defined more by its relationship to a particular place within Great Britain than by its degree of breeding. A growing propensity for moving animals from place to place, and combining existing breeds into new types of livestock, such as Shorthorn cattle or New Leicester sheep, informed these developments.

DNA footprints of livestock domestication and evolutionary history

The observation of animal and plant breeding greatly influenced Darwin's thought. During the maturation of his theory of evolution, he realised that anthropogenic selection was the driving force shaping domestic animal phenotypes to meet human needs. A concept that was transferred to natural species after the reading of Malthus’ book on the struggle for existence. After the definition of his theory, Darwin continuously searched in domestic plant and animals confirmation of his hypotheses on the transmission of traits and evolution of species. He also observed that some morphological and physiological traits were shared among unrelated domestic animal species but were absent in the wild ancestors. The Russian scientist Dmitri Belyaev proved that these traits emerged as a consequence of domestication by recording their appearance in silver fox selected for tame behaviour, an experiment that is ongoing since about 50 years. Nowadays, genomic technologies allow scientists to explore the molecular basis of these traits and to reconstruct the evolutionary history of domestic animals. The availability of high-density single nucleotide polymorphisms panels permits the detection of signatures left by natural and artificial selection along the genome of domestic animals. The analysis of genomic and mitochondrial DNA contributes substantial information for the identification of sites of primary domestication, Neolithic routes of world colonisation and later voyages linked to human migration events. The understanding of all changes occurring following domestication and anthropogenic selection may help in understanding natural selection and molecular evolution occurring in all living organisms.