Phylogenetic trees for primate lice and their vertebrate hosts redrawn from Reed et al . [9]. Trees are shown as cladograms with no branch length information, and are based on molecular and morphological data. Dashed lines between trees represent host-parasite associations. Humans are unique in being parasitized by two genera (Pediculus and Pthirus). (Herd, K.E., Barker, S.C. & Shao, R.(2015))
Photo credits: J. W. Demastes, T. Choe, and V. Smith.
It's a basic principle of evolutionary biology that an obligate commensal, symbiotic or parasitic organism is evolutionary bound to the organism on which it is dependent, It follows then that the genomes of two or more organism in such a relationships will reflect the same major changes which drive evolution.
I have previously described how the evolutionary tree of the human head and body lice, Pediculus humanus, fits exactly on the evolutionary tree of Homo sapiens as we diverged from the common ancestor with chimpanzees. At the same time, our lice diverged from a common ancestor they share with the lice which are obligate parasites on chimpanzees, Pe. schaeffi.
Interestingly, our lice also reflect when we started wearing clothes having lost our body hair. This loss of body hair meant our lice became head lice which are closely related to the chimpanzee's body lice. When we started wearing clothes our lice diverged into two subspecies - head lice, Pe. h. capitis, and body lice, Pe. h. humanus.
And now, something even more interesting and confirmative of evolution, is the discovery that an obligate, symbiont bacteria on which the lice depends, shows exactly the same pattern of divergence, mapped onto the evolutionary tree of the lice.
The symbiotic bacterium, Candidatus Riesia pediculicola, in a typically Heath-Robinson solution to a problem which is a characteristic of mindless, unplanned evolution, and unlike anything an intelligent designer would design, is essential to the lice because they can't make essential B-vitamins and don't get them from the blood on which they exclusively feed.
And, incidentally, these bacteria have evolved by loss of genetic information - something that creationist frauds tell their dupes is impossible because "every loss of genes is invariably fatal" [sic].
This discovery is the subject of a recent open access paper in the journal Molecular Biology & Evolution:
Abstract
Insects have repeatedly forged symbioses with heritable microbes, gaining novel traits. For the microbe, the transition to symbioses can lead to the degeneration of the symbiont's genome through transmission bottlenecks, isolation, and the loss of DNA repair enzymes. However, some insect-microbial symbioses have persisted for millions of years, suggesting that natural selection slows genetic drift and maintains functional consistency between symbiont populations. By sampling in multiple countries, we examine genomic diversity within a symbiont species, a heritable symbiotic bacterium found only in human head lice. We find that human head louse symbionts contain genetic diversity that appears to have arisen contemporaneously with the appearance of anatomically modern humans within Africa and/or during the colonization of Eurasia by humans. We predict that the observed genetic diversity underlies functional differences in extant symbiont lineages, through the inactivation of genes involved in symbiont membrane construction. Furthermore, we find evidence of additional gene losses prior to the appearance of modern humans, also impacting the symbiont membrane. From this, we conclude that symbiont genome degeneration is proceeding, via gene inactivation and subsequent loss, in human head louse symbionts, while genomic diversity is maintained. Collectively, our results provide a look into the genomic diversity within a single symbiont species and highlight the shared evolutionary history of humans, lice, and bacteria.
Introduction
Over the last ∼480 million years (Ma), insects have repeatedly forged relationships with beneficial endosymbionts, that provide them with novel traits (Misof et al. 2014; Sudakaran et al. 2017; McCutcheon et al. 2019). Endosymbiotic bacteria have their genomes reduced, dispensing with genes essential in the non-endosymbiotic progenitor, but expendable in symbiosis (Koskiniemi et al. 2012; Wolf and Koonin 2013; Gil and Latorre 2019.1). The genomes of these endosymbionts also experience the degradation of functions that are relevant to the symbioses, as a product of isolation, transmission bottlenecks, and the loss of some DNA repair enzymes (Moran 1996; McCutcheon and Moran 2012.1). Mutational load will eventually lead to the extinction of the endosymbiont (McCutcheon et al. 2019). Yet, insect-bacterial symbioses can persist for millions of years, suggesting that deterministic processes slow genomic degeneration (Moran et al. 1993, 2008; Allen et al. 2009; O’Brien et al. 2021). Models suggest that individual endosymbiont populations can accrue novel mutations, while natural selection maintains symbiotic functions, across endosymbiont populations (Petterson and Berg 2007). Examination of genetic and functional diversity within an endosymbiont species would provide a critical evaluation of expectations and provide insights into the maintenance of ancient insect-microbial symbioses. To address this problem, we examine global genomic diversity within a single endosymbiont species.
Human head lice (Pediculus humanus; Insecta: Phthirpatera) are obligate ectoparasites of humans, which only consume blood. Like many insect parasites, lice are host to maternally inherited endosymbiotic bacteria, Candidatus Riesia pediculicola (Gammaproteobacteria: Enterobacterales). These endosymbiotic bacteria provide the lice with essential B-vitamins, which the lice cannot obtain from human blood in sufficient quantities to sustain development (Puchta 1955; Buchner 1965; Koch 1967; Eberle and McLean 1982, 1983; Sasaki-Fukatsu et al. 2006; Perotti et al. 2007.1; Boyd et al. 2017.1; Hammoud et al. 2022). Ca. Riesia was present in the common ancestor of lice parasitizing humans, chimpanzees, and gorillas, establishing that the symbiosis began 13 to 25 Ma (Allen et al. 2007.2; Boyd et al. 2017.1). Lice parasitizing humans, chimpanzees, and gorillas are host to different endosymbionts species, including Ca. Riesia pediculicola in human head and body lice (P. humanus), Ca. Riesia pediculschaeffi in chimpanzee lice (Pediculus schaeffi), Ca. Riesia pthripubis in human pubic lice (Pthirus pubis), and Ca. Riesia sp. GBBU in gorilla lice (Pthirus gorillae; Sasaki-Fukatsu et al. 2006; Allen et al. 2007.2; Boyd et al. 2017.1). Whole genome sequencing and assembly found that the genome Ca. Riesia consist of a primary chromosome, 0.529 to 0.574 Mega base pairs (Mbp) in length, and a smaller circular chromid, 0.006 to 0.007 Mbp in length (the smaller circular chromosome has previously been referred to as the pPAN plasmid; however, we believe that chromid is an accurate description of this chromosome given that appears the chromosome has been maintained as separate chromosomal for millions of years and supports essential metabolism; Harrison et al. 2010; Kirkness et al. 2010.1; Boyd et al. 2014.1, 2017.1). Compared to closely related gammaproteobacteria, Escherichia coli K-12 MG1655 and Sodalis praecaptivus HS1 (which have genomes of 4.639 and 5.159 Mbp in length), the genome of Ca. Riesia is relatively small (Blattner et al. 1997; Clayton et al. 2012.2). Therefore, Ca. Riesia represents an established endosymbiont, which has had its genome reduced. Despite its genome being reduced, Ca. Riesia maintains pathways for vitamin synthesis and minimal cellular function, which are important for maintaining the symbioses (Kirkness et al. 2010.1; Boyd et al. 2017.1). Further degeneration of the genome could impact essential cell functions or functions important to the host.
As part of a project examining the evolutionary history of human head lice, focused on identifying genetic diversity and population structure within lice, whole genome sequencing was performed on human head lice collected in 43 countries, including countries within Africa, the Americas, Australasia (including South Pacific Islands), and Eurasia (House et al. 2023). Previous studies have shown that whole genome sequencing conducted on whole lice often captures the endosymbiont genome, which can be isolated and independently evaluated from the host and contaminate DNA (Boyd et al. 2014.1, 2016, 2017.1). We examined sequence data from human head louse samples described in House et al. (2023), using a mixture of phylogenetic and population level analysis to evaluate endosymbiont haplotype diversity within human head louse samples, the origins of this diversity, endosymbiont population structure, and to make predictions about gene maintenance or loss that could impact the symbiotic function.
Bret M Boyd, Niyomi House, Christopher W Carduck, David L Reed,
Genomic Diversity in the Endosymbiotic Bacteria of Human Head Lice, Molecular Biology and Evolution, 41(4), 2024, msae064, https://doi.org/10.1093/molbev/msae064
Copyright: © 2024 The authors.
Published by Oxford University Press. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)
Apart from the definitive evidence for co-evolution of all three species over hundreds of thousands, even millions of years, and evolution by 'impossible' loss of genes, there are other aspects to this study for creationists to try to ignore or dismiss:
- Firstly there is the complete absence of doubt on the part of the scientists that evolution by natural selection is the only way to understand the observable facts;
- Secondly, there is the Heath-Robinson solution to the problem caused by the lack of required vitamins in human blood and the louse's inability to metabolise it for themselves - an intelligent [sic] designer giving lice a symbiotic bacterium to do the job is an unnecessarily complex solution, when it could have given them the same genes that the bacteria use;
- Thirdly, there is the accurate mapping of the evolutionary tree of the lice and their symbionts onto the evolutionary tree from a common ancestor of chimpanzees and Homo sapiens
- Lastly, there is the impossibility of presenting a process of adaptation to a changing environment by genetic mutations as 'devolution' caused by 'genetic entropy'.
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