DOI: 10.5061/dryad.73n5tb380
title: Data from: Were bed bugs the first urban pest insect? Genome-wide patterns of bed bug demography mirror global human expansion

description: There are calls for research into the historical evolutionary
 relationships between humans and their commensals, as it would greatly
 inform models that predict the spread of pests and diseases under urban
 population expansion. The earliest civilizations emerged ~10,000 years ago
 and created conditions ideal for the establishment and spread of commensal
 urban pests. Commensal relations between humans and pests likely emerged
 with these early civilizations; however, for most species (e.g., German
 cockroach and black rat) these relationships are unlikely to have formed
 prior to 5,000 years ago. Following comparative whole genome analysis of
 bed bugs, Cimex lectularius, belonging to two genetically distinct
 lineages, one associated with bats and the other with humans, coupled with
 demographic modelling, our findings suggest that while their association
 with humans dates back potentially hundreds of thousands of years, a
 dramatic change in the effective population size of the human-associated
 lineage occurred ~13,000 years ago; a pattern not found in the
 bat-associated lineage. The timing and magnitude of the demographic
 patterns provide compelling evidence that the human-associated lineage
 closely tracked the demographic history of modern humans and their
 movement into the first cities. As such, bed bugs may represent the first
 true urban pest insect species.
description: # Were bed bugs the first urban pest insect? Genome-wide patterns of bed
 bug demography mirror global human expansion Dataset DOI:
 [10.5061/dryad.73n5tb380](10.5061/dryad.73n5tb380) ## Description of the
 data and file structure This dataset contains the code required to
 replicate the analyses presented in the associated publication. The
 genomic data are deposited in NCBI short read archives (SRA) under
 Bioproject PRJNA1176704. The short reads are in fasta files which were
 used as input for Bowtie v 2.4.1, variants were inferred and vcf file was
 generated using bcftools 1.11. Sites with &gt;50% missing data were
 removed using vcftools v 0.1.18 and exported as filtered vcf file for
 further analyses. Genetic diversity, π, and Tajima'sD were estimated
 using vcftools with a 1 Kb sliding window, for all samples combined and
 for each lineage separately, and output as a text file for analysis and
 visualization in R v 4.3.0. ### Files and variables #### File:
 BedBugDemography.R **Description:** R program file that includes plotting
 for the figures and PCA generation. #### File: command\_line\_code.txt
 **Description:** Command line used for the programs mentioned in the
 methods #### File: plot\_betapsmc.R **Description:**  R code for plotting
 Supp Figure #### File: README\_bedbug\_betapsmc.sh **Description:** readme
 file to generate beta-psmc analysis #### File: bat3.blueprint
 **Description:** blueprint file for bat lineage staiwayplot 2 analysis
 with 3 generations per year. This was then edited for 4-6 generations and
 re-run for each generation time. #### File: hum3.blueprint
 **Description:** blueprint file for human lineage staiwayplot 2 analysis
 with 3 generations per year. This was then edited for 4-6 generations and
 re-run for each generation time. ## Access information Other publicly
 accessible locations of the data: * **BioProject: Processed** * *
 [PRJNA1176704](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1176704) :
 Cimex lectularius bat and human lineage comparison