ancient_trichuris

This repository contains the analysis workflow for the manuscript entitled “Population genomics of ancient and modern Trichuris trichiura”.

The manuscript is available from bioRxiv and has been accepted for publication at Nature Communications (link to follow).

Abstract The neglected tropical disease trichuriasis is caused by the whipworm Trichuris trichiura, a soil-transmitted helminth that has infected humans for millennia. Today, T. trichiura infects as many as 500 million people, predominantly in communities with poor sanitary infrastructure enabling sustained faecal-oral transmission. Using whole-genome sequencing of geographically distributed worms collected from human and other primate hosts, together with ancient samples preserved in archaeologically-defined latrines and deposits dated up to one thousand years old, we present the first population genomics study of T. trichiura. We describe the continent-scale genetic structure between whipworms infecting humans and baboons relative to those infecting other primates. Admixture and population demographic analyses support a stepwise distribution of genetic variation that is highest in Uganda, consistent with an African origin and subsequent translocation with human migration. Finally, genome-wide analyses between human samples and between human and non-human primate samples reveal local regions of genetic differentiation between geographically distinct populations. These data provide insight into zoonotic reservoirs of human-infective T. trichiura and will support future efforts toward the implementation of genomic epidemiology of this globally important helminth.

The analysis workflow is described here, from which individual workbooks containing code for specific analyses can be accessed.

Workbook:Genome analyses
Workbook:Mapping
Workbook:Kraken
Workbook:DNA damage
Workbook:Genome coverage
Workbook:Variant calling and filtering
Workbook:Sampling sites
Workbook:PCAs
Workbook:ANGSD
Workbook:NGSadmix
Workbook:Treemix
Workbook:Admixtools
Workbook:Population history using SMC++
Workbook:Genome-wide genetic variation
Workbook:Beta-tubulin variation

Any reuse of data or code is encouraged with due acknowledgement, either via citation of the published manuscript (when available) and/or GitHub repository. Comments, suggestions, and discussion are welcome.

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License

This work is licensed under a Creative Commons Attribution 4.0 International License.