78 research outputs found
The genomes of the yaws bacterium, Treponema pallidum subsp. pertenue, of nonhuman primate and human origin are not genomically distinct.
No full textBackgroundTreponema pallidum subsp. pertenue (TPE) is the causative agent of human yaws. Yaws is currently reported in 13 endemic countries in Africa, southern Asia, and the Pacific region. During the mid-20th century, a first yaws eradication effort resulted in a global 95% drop in yaws prevalence. The lack of continued surveillance has led to the resurgence of yaws. The disease was believed to have no animal reservoirs, which supported the development of a currently ongoing second yaws eradication campaign. Concomitantly, genetic evidence started to show that TPE strains naturally infect nonhuman primates (NHPs) in sub-Saharan Africa. In our current study we tested hypothesis that NHP- and human-infecting TPE strains differ in the previously unknown parts of the genomes.Methodology/principal findingsIn this study, we determined complete (finished) genomes of ten TPE isolates that originated from NHPs and compared them to TPE whole-genome sequences from human yaws patients. We performed an in-depth analysis of TPE genomes to determine if any consistent genomic differences are present between TPE genomes of human and NHP origin. We were able to resolve previously undetermined TPE chromosomal regions (sequencing gaps) that prevented us from making a conclusion regarding the sequence identity of TPE genomes from NHPs and humans. The comparison among finished genome sequences revealed no consistent differences between human and NHP TPE genomes.Conclusion/significanceOur data show that NHPs are infected with strains that are not only similar to the strains infecting humans but are genomically indistinguishable from them. Although interspecies transmission in NHPs is a rare event and evidence for current spillover events is missing, the existence of the yaws bacterium in NHPs is demonstrated. While the low risk of spillover supports the current yaws treatment campaign, it is of importance to continue yaws surveillance in areas where NHPs are naturally infected with TPE even if yaws is successfully eliminated in humans
Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation
No full textAbstract Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation
Mito-phylogenetic relationship of the new subspecies of gentle monkey Cercopithecus mitis manyaraensis, Butynski & De Jong, 2020
No full textIn 2020, a new subspecies was described in the Cercopithecus mitis complex, the Manyara monkey C. m. manyaraensis, Butynski & De Jong, 2020. The internal taxonomy of this species complex is still debated, and the phylogenetic relationships among the taxa are unclear. Here we provide the first mitochondrial sequence data for C. m. manyaraensis to determine its position within the mitochondrial phylogeny of C. mitis. This subspecies clusters within the youngest (internal divergences between 1.01 and 0.42 Ma) of three main taxonomic clades of C. mitis. Its sister lineages are C. m. boutourlinii (Ethiopia), C. m. albotorquatus (Kenya and Somalia), C. m. albogularis (Kenya and Tanzania), and C. m. monoides (Tanzania and Mozambique). In general, the phylogenetic tree of C. mitis based on mitochondrial sequence data indicates several paraphyletic relationships within the C. mitis complex. As in other African cercopithecines (e.g. Papio and Chlorocebus), these data are suitable for reconstructing historic biogeographical patterns, but they are only of limited value for delimitating taxa
Whole-genome sequencing reveals evidence for inter-species transmission of the yaws bacterium among nonhuman primates in Tanzania
No full textBackground Treponema pallidum subspecies pertenue ( TPE ) is the causative agent of human and nonhuman primate (NHP) yaws infection. The discovery of yaws bacterium in wild populations of NHPs opened the question of transmission mechanisms within NHPs, and this work aims to take a closer look at the transmission of the disease. Methodology/Principal Findings Our study determined eleven whole TPE genomes from NHP isolates collected from three national parks in Tanzania: Lake Manyara National Park (NP), Serengeti NP, and Ruaha NP. The bacteria were isolated from four species of NHPs: Chlorocebus pygerythrus (vervet monkey), Cercopithecus mitis (blue monkey), Papio anubis (olive baboon), and Papio cynocephalus (yellow baboon). Combined with previously generated genomes of TPE originating from NHPs in Tanzania (n = 11), 22 whole-genome TPE sequences have now been analyzed. Out of 231 possible combinations of genome-to-genome comparisons, five revealed an unexpectedly high degree of genetic similarity in samples collected from different NHP species, consistent with inter-species transmission of TPE among NHPs. We estimated a substitution rate of TPE of NHP origin, ranging between 1.77 × 10 -7 and 3.43 × 10 -7 per genomic site per year. Conclusions/Significance The model estimations predicted that the inter-species transmission happened recently, within decades, roughly in an order of magnitude shorter time compared to time needed for the natural diversification of all tested TPE of Tanzanian NHP origin. Moreover, the geographical separation of the sampling sites (NPs) does not preclude TPE transmission between and within NHP species.Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659National Institute of Virology and Bacteriolog
Mathematical modelling Treponema infection in free-ranging Olive baboons (Papio anubis) in Tanzania
No full texthttp://dx.doi.org/10.13039/100000001 National Science Foundationhttp://dx.doi.org/10.13039/100009226 National Security Agencyhttp://dx.doi.org/10.13039/501100001659 Deutsche Forschungsgemeinschaf
Strain diversity of Treponema pallidum subsp. pertenue suggests rare interspecies transmission in African nonhuman primates
No full textSequence analysis of <i>tpr</i>C, D, F, and I genes.
No full textA. Visualization of the full-length tprC, D, F, and I genes, including gene sequences marked as sections (a–g, shown in grey, seven in total). Each section was defined as a DNA region containing two or more nucleotide sequences that differ in three and more positions. Black lines denote positions of single nucleotide variants (SNVs) at the start and at the end of each section. Single nucleotide variants not following the pattern of the section detected within and outside sections are shown as red lines. B. Modular structure of tprC, D, F, and I genes. White and grey show the two different versions of the DNA regions. Dark grey represents the tprD2 allele. Different sequence versions of the sections are combined into different patterns of the tprC, D, F, and I genes in different TPE isolates. In general, the tprF and tprI genes in TPE isolated from NHPs show more variability in combining different versions of the sections compared to TPE of human origin. The Fribourg-Blanc isolate, CDC-2, Samoa D, and Kampung Dalan K363 have identical modular structures of tprC, D, F, and I. C. Coordinates of the tprC, D, F, and I genes with respect to the LMNP-1 reference. D. Section coordinates according to tprC gene coordinates of LMNP-1 reference and the number of SNVs differentiating sections as well as the number of additional SNVs.</p
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