Introduction
The study of organisms that are obligately or facultatively associated with humans can provide insight into the history of its host. For example, human head lice have been used as markers of the past to uncover prehistoric contact between extinct and anatomically modern humans (AMH) (Reed et al., 2004), the timing of the split between human and chimpanzees (5-7 Ma) (Reed et al., 2007), and the origin of clothing use by AMH (Kittler et al., 2003; Toups et al., 2011). The human head louse Pediculus humanus capitis De Geer, 1778 (Phthiraptera: Anoplura) is a permanent, blood-feeding ectoparasite of humans completing their entire life cycle on their human host. Lice cannot live off their host for more than 36 hours (Burkhart & Burkhart, 2007), making their life cycle closely tied to their hosts for thousands of generations. Head lice are primarily found among school-aged children and dispersal (transmission) from one head to another occurs mainly when the host individuals have close physical contact (Mumcuoglu et al., 2021). Ancient human populations also carried lice, and this is demonstrated by the finding of nits still attached to ancient human hair as well as trapped in the combs used (Amanzougaghene et al., 2016; Arriaza et al., 2014; Pedersen et al., 2022). Therefore, host migration and contact should define the population structure of lice. Historically, this appears to be true, that the evolutionary history of human lice appears to have been shaped by human migration (Ewing, 1926; Pedersen et al., 2022) that facilitated host-switching (Reed et al., 2007). However, the increase in ease of global migration and travel could break down geographical barriers and erase historical population structure. The question remains, is louse population structure defined by geographic regions and historic migration or recent host movement.
Anatomically modern humans migrated out of Africa 60-70 thousand years ago (Carto et al., 2009; Stringer, 2000; Walter et al., 2000). A growing number of studies now support two main dispersal events out of Africa: a Southern route to Southeast Asia and a Northern route to Eurasia (Reyes-Centeno et al., 2014; Tassi et al., 2015). As AMHs dispersed throughout Eurasia they interbred with other species of archaic humans including Neanderthals and Denisovans who migrated out of Africa much earlier (Reich et al., 2011; Sankararaman et al., 2014; Villanea & Schraiber, 2019). While genetic and archeological evidence has increased our understanding of human evolution, a complete picture remains elusive because behavior and dispersal are hard to discern from fossilized remains.
As speciation happens in the host lineage, host-specific parasites like lice often speciate in tandem as a result of imposed isolation (Reed et al., 2007). Therefore, the processes shaping human evolution may leave a signal in the genome of human lice. To date, genetic diversity and population structure of head lice has mostly been examined in terms of mitochondrial clade diversity and distribution (Al-Shahrani et al., 2017; Amanzougaghene et al., 2016; Ashfaq et al., 2015; Boumbanda Koyo et al., 2019). Mitochondrial genes; partial cytochrome b and cytochrome oxidase I of lice showed six genetically distinct, geographically unique clades (clades A-F). Clade A is distributed world-wide, while the other clades are more geographically restricted. Clade B is found in Europe, the Americas, and Australia. Clade C is found in Africa and southern Asia. Clades D and E are found only in Africa, while Clade F has been found on individuals in Argentina and Mexico (Amanzougaghene et al., 2019). Of these clades, only A and D include both head and body lice, while the rest of the clades have consisted only of head lice.
Although identifying the distribution of mitochondrial clades through only fragments of genes has helped elucidate the possibility of a demographic history of human head lice, these patterns are only vaguely indicative of just the maternal louse lineages, and longer term co-speciating and coevolutionary events. An understanding of genome-wide patterns of genetic diversity and population structure across global head louse populations are needed to characterize the complete picture of louse evolutionary history. For example, considering that lice are horizontally transmitted, it is unclear if the nuclear genetic structure of the lice mirrors that of its host genetic population structure, or if human migrations and more recently the ease of global travel has erased these patterns by transporting lice around the world. The question remains whether lice are more defined by geography or host movement. Given the long history of human migration across the globe, and the co-demography observed in lice (Reed et al., 2007), it is useful to evaluate worldwide louse populations as geographical units (i.e., countries or continents) rather than genetic clades. Investigating population structure across geographically separated populations using neutral nuclear loci can show interactions between genetic drift and gene flow (Slatkin, 1987) that may not be captured by uniparentally inherited markers (i.e., mitochondrial DNA) (Ebert & Fields, 2020).
In attempts to understand the nuclear genetic diversity of human lice, a previous study used microsatellite markers from 93 specimens in 11 countries and found no relationship between the mitochondrial clades and the nuclear population clusters (Ascunce et al., 2013). Additionally, these microsatellite markers were able to detect geographically structured genetic population clusters indicating low levels of gene flow between global louse populations (Ascunce et al., 2013). Further investigations with a much broader sampling regime including genome-wide representation are needed to have the resolution to identify the distribution of genetic variants as well as the genetic population structure of the global human head louse populations.
Using the human body louse, Pediculus humanus humanus genome as a reference, we analyzed whole nuclear genomes of the human head louseP. humanus capitis from across the world to overcome the current lack of geographic and genome-wide representation. The main goals of this study were to: 1) investigate nuclear genetic diversity across the globe ; 2) examine the geographic distribution of genetic variants worldwide ; 3) identify the population structure based on nuclear markers; and 4) investigate possible modes of gene flow and historical population connectivity between global louse populations. Our main questions are, does the population structure of human lice match that of its host migration patterns or does it reflect the same evolutionary history shown through its mitochondrial genome?