Amplification and sequencing of entire tick mitochondrial genomes for a phylogenomic analysis

Identification and characterization of a novel Pavlovskyella (Acari: Argasidae) from Chile, parasite of the culpeo fox (Lycalopex culpaeus)

Soft ticks (Argasidae) of the subgenus Pavlovskyella Pospelova-Shtrom are worldwide distributed parasites of medical importance. However, the systematics of the subgenus are currently under debate because genetic data shows that the group is paraphyletic. Meanwhile, species of Pavlovskyella continue to be discovered. In this study a novel species of the subgenus is described from specimens collected on a fox in central Chile. The larva of this new species differentiates from other Pavlovskyella spp. by having the following combination of characters: subpyriform dorsal plate; 15 pairs of setae, 7 anterolateral, 3 central, and 5 posterolateral, and hypostome with denticles in the distal third. Nymphs and adults of the species lack cheeks, eyes or bulging structures on the flank, but exhibit dorsoventral grooves, and humps on tarsi I, II, and III. Moreover, a patch of glabrous integument appears on the distal portion of coxal folds. A phylogenetic analysis using the mitogenome indicates a monophyletic group composed by Ornithodoros (Pavlovskyella) brasiliensis Aragão, Ornithodoros (Pavlovskyella) furcosus Neumann, Ornithodoros (Pavlovskyella) improvisus Muñoz-Leal & Venzal, and Ornithodoros (Pavlovskyella) rostratus Aragão. Interestingly, a phylogeny using 18S-28S rDNA sequences shows that South American Pavlovskyella spp. are paraphyletic, as depicted in previous studies. Adding species of the subgenus from the Neotropical region to phylogenetic analyses could aid to solve this paraphyly. Furthermore, this is the fifth species of Pavlovskyella described in South America, and the second in Chile.

Pathogen and Host Associations of Soft Ticks Collected in South Texas

Background: Soft ticks (Family: Argasidae) are vectors of relapsing fever Borrelia in the United States and are potential vectors of African swine fever virus, a pathogen that could have a devastating effect on the U.S. swine industry if introduced to the U.S. mainland. Much of the tick-borne disease research in the U.S. focuses on hard ticks, and less is known about the ecology of soft ticks. Some soft tick species found in the southern U.S. have a wide host range and may feed on cattle, swine, native and exotic ungulates, small mammals, reptiles, and humans. Because the feeding habit of most soft tick species involves taking short, repeated blood meals that may include multiple host species, pathogen transmission among hosts is a concern both for human and animal health. Materials and Methods: Sampling was carried out at four locations in south Texas using dry ice traps placed in or near animal burrows and other sheltering cracks and crevasses that may provide refuge for soft ticks. Collected ticks were identified and subsequently screened for Rickettsia and Borrelia species and for host bloodmeal detection using conventional polymerase chain reaction and Sanger sequencing for pathogen and host species identification. Results: In total, 256 ticks of two Ornithodorinae species were screened. Borrelia species were identified in three samples. Bloodmeal detections were made in 22 tick specimens, representing eight vertebrate host species. Conclusions: Results demonstrate that the soft tick species detected herein feed on a range of wildlife hosts in south Texas and are associated with agents of human disease.

Mitochondrial genome analysis across different populations reveals the intraspecific variation and phylogeography of the Caucasian soft tick relapsing fever vector, Ornithodoros (Pavlovskyella) verrucosus (Ixodida: Argasidae)

Territories in southern parts of Eastern Europe and in the Caucasus are endemic for tick-borne relapsing fever (TBRF), caused by Borrelia caucasica. This spirochete is transmitted exclusively by the bites of Ornithodoros verrucosus; however, the distribution and genetic diversity of the tick vector have not been explored. To address this, we performed a phylogeographic study of O. verrucosus specimens collected across a large geographic distribution. We sequenced and analyzed complete mitochondrial genomes of 54 individual O. verrucosus ticks representing 23 geographically diverse populations from Ukraine, Georgia, and Azerbaijan. We detected 47 unique haplotypes, with every collection site exhibiting distinct polymorphisms. This, along with other population genetic indices, suggests little evidence of gene flow between populations. The Bayesian coalescent analysis revealed the presence of four lineages that diverged in the Middle Pleistocene (770-126 kya). Two lineages were widespread and present in all study regions, while the other two were restricted to the southern foothills of the Lesser Caucasus mountain range. The sympatry of these ancient lineages suggests that isolation by environment, in addition to geographic distance, may play a role in the intraspecific divergence of tick populations. Using a phylogeographic approach, we provide a snapshot of genetic diversity in O. verrucosus and discuss the evolutionary history of the tick vector.

Description of Ornithodoros (Pavlovskyella) tartakovskyi using scanning electron microscopy, with notes on the morphology of Pavlovskyella sensu stricto and Theriodoros subgenera

Accumulation of DNA sequence data and its use in systematics of the family Argasidae reveals new incongruencies between genera and subgenera, since several groups defined by classical taxonomy appear to be paraphyletic, which is the case of the subgenus Pavlovskyella. In order to identify morphological characters unique to one of the monophyletic groupings within Pavlovskyella and improve its system, we describe all active stages of Ornithodoros (Pavlovskyella) tartakovskyi, a species with an incomplete original description. Larvae, nymphs, males and females from Iran were examined with scanning electron microscopy (SEM). The larva of O. (P.) tartakovskyi lacks dorsal plate, posteromedian seta, postcoxal setae and a spinose area in palpal article I; the dorsal surface has 13 pairs of setae and the hypostome has two short rows of denticles in the apex only. The first nymphal instar (N1) has a micromammillated body with faint dorsal and ventral disks. The second nymphal instar (N2) shows mammillated body with an incipient hood, and dorsal disks outlined as in subsequent instars. Both N1 and N2 have a small patch of glabrous surface in the anterior margin of preanal groove, absent in posterior stages. Third nymphal instar (N3) has a small hood and lack cheeks, which are incipient in the fourth nymphal instar (N4). The four nymphal instars (N1-N4) have blunt hypostomes, striated capitula, non-mammillated legs, and 3 humps on tarsi I. Females and males of O. (P.) tartakovskyi have mammillated bodies, small cheeks not covering the capitulum, the anteromedian disk is placed anteriorly to anterior central disks, and a posterior median file of disks is merged with the median disk. We describe all postembryonic stages of O. (P.) tartakovskyi providing morphological characters that define Pavlovskyella sensu stricto and Theriodoros, a sister subgenus that includes similarly shaped species.

Identification of non-model mammal species using the MinION DNA sequencer from Oxford Nanopore

Background

The Neotropics harbors the largest species richness of the planet; however, even in well-studied groups, there are potentially hundreds of species that lack a formal description, and likewise, many already described taxa are difficult to identify using morphology. Specifically in small mammals, complex morphological diagnoses have been facilitated by the use of molecular data, particularly from mitochondrial sequences, to obtain accurate species identifications. Obtaining mitochondrial markers implies the use of PCR and specific primers, which are largely absent for non-model organisms. Oxford Nanopore Technologies (ONT) is a new alternative for sequencing the entire mitochondrial genome without the need for specific primers. Only a limited number of studies have employed exclusively ONT long-reads to assemble mitochondrial genomes, and few studies have yet evaluated the usefulness of such reads in multiple non-model organisms.

Methods

We implemented fieldwork to collect small mammals, including rodents, bats, and marsupials, in five localities in the northern extreme of the Cordillera Central of Colombia. DNA samples were sequenced using the MinION device and Flongle flow cells. Shotgun-sequenced data was used to reconstruct the mitochondrial genome of all the samples. In parallel, using a customized computational pipeline, species-level identifications were obtained based on sequencing raw reads (Whole Genome Sequencing). ONT-based identifications were corroborated using traditional morphological characters and phylogenetic analyses.

Results

A total of 24 individuals from 18 species were collected, morphologically identified, and deposited in the biological collection of Universidad EAFIT. Our different computational pipelines were able to reconstruct mitochondrial genomes from exclusively ONT reads. We obtained three new mitochondrial genomes and eight new molecular mitochondrial sequences for six species. Our species identification pipeline was able to obtain accurate species identifications for up to 75% of the individuals in as little as 5 s. Finally, our phylogenetic analyses corroborated the identifications from our automated species identification pipeline and revealed important contributions to the knowledge of the diversity of Neotropical small mammals.

Discussion

This study was able to evaluate different pipelines to reconstruct mitochondrial genomes from non-model organisms, using exclusively ONT reads, benchmarking these protocols on a multi-species dataset. The proposed methodology can be applied by non-expert taxonomists and has the potential to be implemented in real-time, without the need to euthanize the organisms and under field conditions. Therefore, it stands as a relevant tool to help increase the available data for non-model organisms, and the rate at which researchers can characterize life specially in highly biodiverse places as the Neotropics.

Novel Rickettsia and host records for argasid ticks, including Alveonasus cooleyi, on wild mammals in Baja California, Mexico

We conducted surveillance of mammals to investigate their associations with argasid ticks and tick-borne pathogens. During 2021, a total of 20 wild carnivores and 57 lagomorphs were sampled, and 39 argasid ticks belonging to two species were collected. All mammals and ticks were tested by molecular assays to detect Borrelia and Rickettsia infections. Nine ticks identified as Otobius megnini were collected from two coyotes (Canis latrans) and 30 Alveonasus cooleyi (McIvor 1941) were collected from six bobcats (Lynx rufus) and one rabbit (Sylvilagus auduboni). We detected Rickettsia spp. DNA in 21 of the 27 (77.8%) tested Av. cooleyi and none of the O. megnini. No ticks were PCR-positive for borreliae and all mammals were PCR-negative for both pathogen genera. Phylogenetic analysis based on gltA, htrA, and 16 S rRNA targets revealed that all rickettsiae from Av. cooleyi clustered with ancestral group rickettsiae, likely representing a novel species of possibly endosymbiotic Rickettsia. The significance of Av. cooleyi and the newly identified Rickettsia sp. to the health of wildlife is unknown, and further work is indicated to determine whether they may be relevant to public health or carnivore conservation.

Mitochondrial genome and nuclear ribosomal RNA analysis place Alveonasus lahorensis within the Argasinae and suggest that the genus Alveonasus is paraphyletic

Two major families exist in ticks, the Argasidae and Ixodidae. The Argasidae comprise 2 sub-families, Argasinae and Ornithodorinae. The placement into subfamilies illuminate differences in morphological and molecular systematics and is important since it provides insight into evolutionary divergence within this family. It also identifies fundamental gaps in our understanding of argasid evolution that provide directions for future research. Molecular systematics based on mitochondrial genomics and 18S/28S ribosomal RNA confirmed the placement of various genera and subgenera into the Argasinae: Argas (including Argas and Persicargas), Navis, Ogadenus, Otobius lagophilus, Proknekalia, Secretargas and the Ornithodorinae: Alectorobius, Antricola (including Antricola and Parantricola), Carios, Chiropterargas, Nothoaspis, Ornithodoros (including Microargas, Ornamentum, Ornithodoros sensu strictu, Pavlovskyella), Otobius sensu strictu, Reticulinasus and Subparmatus. The position of Alveonasus remains controversial since traditional taxonomy placed it in the Ornithodorinae, while cladistic and limited molecular analysis placed it in the Argasinae. The current study aimed to resolve the systematic position of Alveonasus using mitochondrial genomic and 18S/28S ribosomal RNA systematics by sequencing the type species Alveonasus lahorensis from Pakistan. In addition, the mitochondrial genomes for Argas reflexus and Alectorobius kelleyi are reported from Germany and the USA, respectively. The systematic data unambiguously place Alveonasus in the Argasinae and also suggest that Alveonasus may be another paraphyletic genus.

Description of a new Ornithodoros (Pavlovskyella) (Ixodida: Argasidae) tick species from Pakistan

The genus Ornithodoros is notably diverse within the family Argasidae, comprising approximately 134 species distributed among 4 subgenera, 1 of which is the subgenus Pavlovskyella. In an earlier study, we identified distinct soft ticks as Ornithodoros (Pavlovskyella) sp., which were collected from animal shelters in Khyber Pakhtunkhwa, Pakistan. Providing additional collections from that same locality and a comprehensive analysis involving detailed morphological and mitogenome-based comparisons with closely related species, this study formally designates a novel species for these specimens. Adults and late-instar nymphs of the new species display a dorsoventral groove, small cheeks not covering the capitulum, 5 small even humps on tarsus I and a transverse postanal groove intersecting the median postanal groove perpendicularly. It also lacks a tuft of setae on the ventral surface of the hood which separates the novel species from Ornithodoros papillipes. Ventral chaetotaxy of tarsus IV indicates 4–7 setal pairs in nymphs and 5–7 pairs in adults that separate the new species from Ornithodoros tholozani sensu stricto and Ornithodoros crossi, 2 morphologically closely related species that occur in geographical proximity. Phylogenetic analyses of the full-length mitochondrial genome and the 18S and 28S ribosomal RNA genes, combined with pairwise nucleotide comparisons of cox1, cox2, atp8, atp6, cox3, nad3, nad5, nad4, nad4L, nad6, cytb, nad1, nad2, 12S rDNA, 16S rDNA, 18S rDNA and 28S rDNA further support that the new species belongs to the Pavlovskyella subgenus, clustering with O. tholozani, Ornithodoros verrucosus and Ornithodoros tartakovskyi.

American mitogenome reference for the tropical brown dog tick, Rhipicephalus linnaei (Audouin, 1826)

The brown dog tick, Rhipicephalus linnaei (Audouin, 1826), is distributed across the American continent and is formerly known as the "tropical lineage". It belongs to the Rhipicephalus sanguineus (Latreille, 1806) species complex, referred to as R. sanguineus (sensu lato). Mitochondrial genome sequences are frequently used for the identification and represent reference material for field studies. In the present study, the entire mitochondrial genomes of R. linnaei (∼15 kb) collected from dogs in Mexico were sequenced and compared with available mitogenomes of R. sanguineus (s.l.). The mitochondrial genome is ∼90% identical to the reference genome of R. sanguineus (sensu stricto, former "temperate lineage") and > 99% identical to R. linnaei mitogenome derived from the neotype. Two additional mitogenomes were obtained and described as R. linnaei and R. turanicus from dogs in Saudi Arabia. The present study delivers a molecular reference for R. linnaei from America and complements R. linnaei mitogenomes from Africa, Asia and Australia. We propose to consider the complete mitogenome, as the reference for American R. linnaei, even when partial mitochondrial cox1, 12S rRNA or 16S rRNA genes are characterised.

New records of soft ticks (Acari: Argasidae) from caves in Brazil, with a morphological study of Ornithodoros fonsecai and an analysis of the taxonomic status of Antricola inexpectata

In this study, we report soft ticks from bat-inhabiting caves in different areas of Brazil. From 2010 to 2019, we collected 807 tick specimens from nine caves located in four Brazilian states among two biomes. Ticks were morphologically identified as Antricola guglielmonei (282 specimens), Ornithodoros cavernicolous (260 specimens), and Ornithodoros fonsecai (265 specimens). Whereas A. guglielmonei was collected on bat guano in hot caves, O. cavernicolous and O. fonsecai were collected in cracks and crevices on the walls of cold caves, sometimes in the same chamber. Morphological identifications were corroborated by molecular and phylogenetic analyses inferred from tick mitochondrial 16S rRNA gene partial sequences. The sequences of A. guglielmonei, O. cavernicolous and O. fonsecai collected in this study clustered with conspecific GenBank sequences from different localities of Brazil. Remarkably, a clade containing 12 sequences of O. fonsecai was clearly bifurcated, denoting a degree of genetic divergence (up to 5 %) of specimens from Cerrado/Atlantic Forest biomes with the specimens from the Caatinga biome. To further evaluate this divergence, we performed morphometric analysis of the larval stage of different O. fonsencai populations by principal component analysis, which indicated that the larvae from Caatinga populations were generally smaller than the larvae from other biomes. Some of the present A. guglielmonei specimens were collected from the type locality of Antricola inexpectata. Comparisons of these specimens with the type specimens of A. inexpectata and A. guglielmonei indicated that they could not be separated by their external morphology. Hence, we are relegating A. inexpectata to a synonym of A. guglielmonei. This proposal is corroborated by our phylogenetic analysis.

New insights into the molecular phylogeny, biogeographical history, and diversification of Amblyomma ticks (Acari: Ixodidae) based on mitogenomes and nuclear sequences

BACKGROUND

Amblyomma is the third most diversified genus of Ixodidae that is distributed across the Indomalayan, Afrotropical, Australasian (IAA), Nearctic and Neotropical biogeographic ecoregions, reaching in the Neotropic its highest diversity. There have been hints in previously published phylogenetic trees from mitochondrial genome, nuclear rRNA, from combinations of both and morphology that the Australasian Amblyomma or the Australasian Amblyomma plus the Amblyomma species from the southern cone of South America, might be sister-group to the Amblyomma of the rest of the world. However, a stable phylogenetic framework of Amblyomma for a better understanding of the biogeographic patterns underpinning its diversification is lacking.

METHODS

We used genomic techniques to sequence complete and nearly complete mitochondrial genomes -ca. 15 kbp- as well as the nuclear ribosomal cluster -ca. 8 kbp- for 17 Amblyomma ticks in order to study the phylogeny and biogeographic pattern of the genus Amblyomma, with particular emphasis on the Neotropical region. The new genomic information generated here together with genomic information available on 43 ticks (22 other Amblyomma species and 21 other hard ticks-as outgroup-) were used to perform probabilistic methods of phylogenetic and biogeographic inferences and time-tree estimation using biogeographic dates.

RESULTS

In the present paper, we present the strongest evidence yet that Australasian Amblyomma may indeed be the sister-group to the Amblyomma of the rest of the world (species that occur mainly in the Neotropical and Afrotropical zoogeographic regions). Our results showed that all Amblyomma subgenera (Cernyomma, Anastosiella, Xiphiastor, Adenopleura, Aponomma and Dermiomma) are not monophyletic, except for Walkeriana and Amblyomma. Likewise, our best biogeographic scenario supports the origin of Amblyomma and its posterior diversification in the southern hemisphere at 47.8 and 36.8 Mya, respectively. This diversification could be associated with the end of the connection of Australasia and Neotropical ecoregions by the Antarctic land bridge. Also, the biogeographic analyses let us see the colonization patterns of some neotropical Amblyomma species to the Nearctic.

CONCLUSIONS

We found strong evidence that the main theater of diversification of Amblyomma was the southern hemisphere, potentially driven by the Antarctic Bridge's intermittent connection in the late Eocene. In addition, the subgeneric classification of Amblyomma lacks evolutionary support. Future studies using denser taxonomic sampling may lead to new findings on the phylogenetic relationships and biogeographic history of Amblyomma genus.

Description of a new Pavlovskyella species (Acari: Argasidae) from Chile

Soft ticks (Argasidae) of the Pavlovskyella Pospelova-Shtrom subgenus are important vectors of relapsing fever spirochetes, which are agents of disease globally. South American representatives of the Pavlovskyella subgenus include 3 species: Ornithodoros (Pavlovskyella) brasiliensis Aragão, Ornithodoros (Pavlovskyella) furcosus Neumann, and Ornithodoros (Pavlovskyella) rostratus Aragão. Here, we describe a fourth species based on morphological and mitogenomic evidence of ticks collected in burrows of unknown hosts in central Chile. The larva of the new species separates from other South American soft ticks by the following combination of characters: 13 pairs of dorsolateral setae, dorsal plate hexagonal, hypostome blunt with denticles from apex almost to the base. Adults of this new species lack cheeks, possess a dorsoventral groove, and have humps, similar to O. (P.) brasiliensis; however, they lack bulging structures on the flanks of idiosoma. Moreover, females and males differ from O. (P.) rostratus by having 3 humps instead of spurs in tarsi I and from O. (P.) furcosus because of their smaller size and thinner anterior lip of the genital aperture in females. The phylogenetic analysis performed with mitogenomes of the Argasidae family depicts the new Pavlovskyella species from Chile in a monophyletic clade with other South American species in the subgenus, confirming a regional group.

Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates

Genome skimming is defined as low-pass sequencing below 0.05× coverage and is typically used for mitochondrial genome recovery and species identification. Long-read nanopore sequencers enable simultaneous reading of both DNA sequence and methylation and can multiplex samples for low-cost genome skimming. Here I present nanopore sequencing as a highly precise platform for global DNA methylation and transposon assessment. At coverage of just 0.001×, or 30 Mb of reads, accuracy is sub-1%. Biological and technical replicates validate high precision. Skimming 40 vertebrate species reveals conserved patterns of global methylation consistent with whole-genome bisulfite sequencing and an average mapping rate >97%. Genome size directly correlates to global DNA methylation, explaining 39% of its variance. Accurate SINE and LINE transposon methylation in both the mouse and primates can be obtained with just 0.0001× coverage, or 3 Mb of reads. Sample multiplexing, field portability, and the low price of this instrument combine to make genome skimming for DNA methylation an accessible method for epigenetic assessment from ecology to epidemiology and for low-resource groups.

Highly-multiplexed and efficient long-amplicon PacBio and Nanopore sequencing of hundreds of full mitochondrial genomes

BACKGROUND

Mitochondrial genome sequences have become critical to the study of biodiversity. Genome skimming and other short-read based methods are the most common approaches, but they are not well-suited to scale up to multiplexing hundreds of samples. Here, we report on a new approach to sequence hundreds to thousands of complete mitochondrial genomes in parallel using long-amplicon sequencing. We amplified the mitochondrial genome of 677 specimens in two partially overlapping amplicons and implemented an asymmetric PCR-based indexing approach to multiplex 1,159 long amplicons together on a single PacBio SMRT Sequel II cell. We also tested this method on Oxford Nanopore Technologies (ONT) MinION R9.4 to assess if this method could be applied to other long-read technologies. We implemented several optimizations that make this method significantly more efficient than alternative mitochondrial genome sequencing methods.

RESULTS

With the PacBio sequencing data we recovered at least one of the two fragments for 96% of samples (~ 80-90%) with mean coverage ~ 1,500x. The ONT data recovered less than 50% of input fragments likely due to low throughput and the design of the Barcoded Universal Primers which were optimized for PacBio sequencing. We compared a single mitochondrial gene alignment to half and full mitochondrial genomes and found, as expected, increased tree support with longer alignments, though whole mitochondrial genomes were not significantly better than half mitochondrial genomes.

CONCLUSIONS

This method can effectively capture thousands of long amplicons in a single run and be used to build more robust phylogenies quickly and effectively. We provide several recommendations for future users depending on the evolutionary scale of their system. A natural extension of this method is to collect multi-locus datasets consisting of mitochondrial genomes and several long nuclear loci at once.

Paradigms in tick evolution

The study of tick evolution may be classified into disciplines such as taxonomy and systematics, biogeography, evolution and development (evo-devo), ecology, and hematophagy. These disciplines overlap and impact each other to various extents. Advances in one field may lead to paradigm shifts in our understanding of tick evolution not apparent to other fields. The current study considers paradigm shifts that occurred, are in the process, or may occur in future for the disciplines that study tick evolution. Some disciplines have undergone significant changes, while others may still be developing their own paradigms. Integration of these various disciplines is essential to come to a holistic view of tick evolution; however, maturation of paradigms may be necessary before this vision can be attained.

The “southeastern Europe” lineage of the brown dog tick Rhipicephalus sanguineus (sensu lato) identified as Rhipicephalus rutilus Koch, 1844: Comparison with holotype and generation of mitogenome reference from Israel

The brown dog tick Rhipicephalus sanguineus (sensu lato) in the southeastern Mediterranean region and the Middle East is difficult to identify due to the presence of multiple mitochondrial DNA haplogroup lineages. The purpose of this study was to clarify the identity of the "southeastern Europe" lineage of this tick species complex. Our research shows that female ticks of the "southeastern Europe" lineage correspond to the morphology of R. rutilus Koch, 1844 as found in type-material at the Museum für Naturkunde Berlin in Germany. We characterised the complete mitogenomes of R. rutilus, R. turanicus Pomerantsev, 1940 and Rhipicephalus sanguineus (Latreille, 1806) in order to improve our understanding of the phylogenetic relationships among species within the R. sanguineus (sensu lato) complex. The material associated with the morphology of R. rutilus was previously labelled as the "southeastern Europe" lineage and found in Israel and Egypt, including Lower Egypt and the Nile Delta, where the original type-material was collected. Based on the morphology, genetic identity, and geographical distribution of the species, we conclude that the name R. rutilus is correctly linked to the "southeastern Europe" lineage of R. sanguineus (sensu lato).

Genome Skimming with Nanopore Sequencing Precisely Determines Global and Transposon DNA Methylation in Vertebrates

Genome skimming is defined as low-pass sequencing below 0.05X coverage and is typically used for mitochondrial genome recovery and species identification. Long read nanopore sequencers enable simultaneous reading of both DNA sequence and methylation and can multiplex samples for low-cost genome skimming. Here I present nanopore sequencing as a highly precise platform for global DNA methylation and transposon assessment. At coverage of just 0.001X, or 30 Mb of reads, accuracy is sub-1%. Biological and technical replicates validate high precision. Skimming 40 vertebrate species reveals conserved patterns of global methylation consistent with whole genome bisulfite sequencing and an average mapping rate above 97%. Genome size directly correlates to global DNA methylation, explaining 44% of its variance. Accurate SINE and LINE transposon methylation in both mouse and primates can be obtained with just 0.0001X coverage, or 3 Mb of reads. Sample multiplexing, field portability, and the low price of this instrument combine to make genome skimming for DNA methylation an accessible method for epigenetic assessment from ecology to epidemiology, and by low resource groups.