Preston, S. G. | Search bioRxiv

bioRxiv2020

Alpha globin variation in the long-tailed macaque suggests malaria selection

Human haemoglobin variants, such as sickle, confer protection against death from malaria; consequently, frequencies of such variants are often greatly elevated in humans from malaria endemic regions. Among non-human primates, the long-tailed macaque, Macaca fascicularis, also displays substantial haemoglobin variation. Almost all M. fascicularis haemoglobin variation is in the alpha globin chain, encoded by two linked genes: HBA1 and HBA2. We demonstrate that alpha globin variation in M. fascicularis correlates with the strength of malaria selection. We identify a range of missense mutations in M. fascicularis alpha globin and demonstrate that some of these exhibit a striking HBA1 or HBA2 specificity, a pattern consistent with computational simulations of selection on genes exhibiting copy number variation. We propose that M. fascicularis accumulated amino acid substitutions in its alpha globin genes under malaria selection, in a process that closely mirrors, but does not entirely converge with, human malaria adaptation.

evolutionary biology↗

bioRxiv2020

Deep sequencing reveals Campylobacter in commercial meat chickens less than 8 days old.

Campylobacter from contaminated poultry meat is a major source of human gastroenteritis worldwide. To date, attempts to control this zoonotic infection with on-farm biosecurity measures have been inconsistent. A cornerstone of these efforts has been the detection of chicken infection with microbiological culture, which typically does not occur until birds are at least 21 days old. Using molecular methods for detecting Campylobacter presence, 16S microbiome analysis and deep sequencing of the Campylobacter porA gene, Campylobacter can be identified at very low levels in most or all flocks fewer than 8 days old. These young chicks exhibit a much greater diversity of porA types than older birds testing positive for Campylobacter by culture or qPCR. This suggests that, as the bacteria multiply sufficiently to be detected by culture methods, one or two strains, as indicated by porA type, dominate the infection. The findings that (i) most young chicks carry some Campylobacter and (ii) not all flocks become Campylobacter positive by culture, suggests that efforts to control infection should concentrate on how to maintain Campylobacter at low levels by the prevention of the overgrowth of single strains, which ultimately leads to the contamination of food.

microbiology↗