Advancing mite phylogenomics: Designing ultraconserved elements for Acari phylogeny

Dam, Matthew H. Van; Trautwein, Michelle; Spicer, Greg S.; Esposito, Lauren A.

doi:10.1111/1755-0998.12962

Cited by 39 publications

(32 citation statements)

References 70 publications

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“…We are unaware of potential morphological synapomorphies for Acari and Pseudoscorpiones to the exclusion of Solifugae (e.g. the free finger of the chelicera articulating ventrally is shared by all three groups 11 ). In contrast, a potential morphological synapomorphy for Acari and Solifugae is a tight grouping of the epistomo-labral plate and discrete lateral lips around the anteriorly-positioned mouth, shared by this group to the exclusion of pseudoscorpions 36 , and this grouping has been recovered in some morphological cladistic analyses (e.g.…”

Section: Resultsmentioning

confidence: 99%

“…These studies recovered several established high-level groups (Chelicerata, Euchelicerata, and Tetrapulmonata) and intriguingly proposed that the horseshoe crabs might be a secondarily marine, arachnid lineage 9 . Recent studies were unable to provide firm conclusions for the interrelationships between mites and ticks 10,11 , traditionally considered to represent a monophyletic group (Acari). However, morphological support for Acari is not unanimous and the two subgroups have also been suggested to constitute independently evolved lineages: Acariformes and Parasitiformes 10–12 , including the medically important haemophages.…”

Section: Introductionmentioning

confidence: 99%

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Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida

et al. 2019

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Chelicerates are a diverse group of arthropods, represented by such forms as predatory spiders and scorpions, parasitic ticks, humic detritivores, and marine sea spiders (pycnogonids) and horseshoe crabs. Conflicting phylogenetic relationships have been proposed for chelicerates based on both morphological and molecular data, the latter usually not recovering arachnids as a clade and instead finding horseshoe crabs nested inside terrestrial Arachnida. Here, using genomic-scale datasets and analyses optimised for countering systematic error, we find strong support for monophyletic Acari (ticks and mites), which when considered as a single group represent the most biodiverse chelicerate lineage. In addition, our analysis recovers marine forms (sea spiders and horseshoe crabs) as the successive sister groups of a monophyletic lineage of terrestrial arachnids, suggesting a single colonisation of land within Chelicerata and the absence of wholly secondarily marine arachnid orders.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida

et al. 2019

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“…For arachnids, progress has been made in this regard for the most diverse arachnid lineage, Acari (Van Dam, Trautwein, Spicer, & Esposito, ). The arachnid‐specific probe set we used targets 1,120 loci, while the more specific Acari probe set targets 1,832 loci, with increased UCE recovery potentially even in nonacarine arachnids (Van Dam et al, ). Other considerations may certainly help locus recovery, including adjustments to the hybridization protocol (Li, Hofreiter, Straube, Corrigan, & Naylor, ; Paijmans, Fickel, Courtiol, Hofreiter, & Förster, ) and deeper sequencing, particularly for extremely important specimens (e.g., type or rare specimens).…”

Section: Discussionmentioning

confidence: 99%

“…Using probe sets that are more taxon-specific will increase locus recovery and decrease nontarget loci. For arachnids, progress has been made in this regard for the most diverse arachnid lineage, Acari (Van Dam, Trautwein, Spicer, & Esposito, 2019). The arachnid-specific probe set we used targets 1,120 loci, while the more specific Acari probe set targets 1,832 loci, with increased UCE recovery potentially even in nonacarine arachnids (Van Dam et al, 2019).…”

Section: Practical Considerationsmentioning

confidence: 99%

Sequence capture phylogenomics of historical ethanol‐preserved museum specimens: Unlocking the rest of the vault

Derkarabetian

Benavides

Giribet

2019

Molecular Ecology Resources

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Natural history collections play a crucial role in biodiversity research, and museum specimens are increasingly being incorporated into modern genetics‐based studies. Sequence capture methods have proven incredibly useful for phylogenomics, providing the additional ability to sequence historical museum specimens with highly degraded DNA, which until recently have been deemed less valuable for genetic work. The successful sequencing of ultraconserved elements (UCEs) from historical museum specimens has been demonstrated on multiple tissue types including dried bird skins, formalin‐fixed squamates and pinned insects. However, no study has thoroughly demonstrated this approach for historical ethanol‐preserved museum specimens. Alongside sequencing of “fresh” specimens preserved in >95% ethanol and stored at −80°C, we used extraction techniques specifically designed for degraded DNA coupled with sequence capture protocols to sequence UCEs from historical museum specimens preserved in 70%–80% ethanol and stored at room temperature, the standard for such ethanol‐preserved museum collections. Across 35 fresh and 15 historical museum samples of the arachnid order Opiliones, an average of 345 UCE loci were included in phylogenomic matrices, with museum samples ranging from six to 495 loci. We successfully demonstrate the inclusion of historical ethanol‐preserved museum specimens in modern sequence capture phylogenomic studies, show a high frequency of variant bases at the species and population levels, and from off‐target reads successfully recover multiple loci traditionally sequenced in multilocus studies including mitochondrial loci and nuclear rRNA loci. The methods detailed in this study will allow researchers to potentially acquire genetic data from millions of ethanol‐preserved museum specimens held in collections worldwide.

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“…One of these reduced representation methods for isolating homologous loci is sequence capture, also known as targeted capture or hybrid enrichment. This method can isolate many orthologous loci, even from low quality or degraded DNA samples (Hawkins et al, 2016;Knyshov et al, 2019), and has been increasingly used in phylogenetic research of many different groups (Haddad et al, 2018;Courcelle et al, 2019;Liu et al, 2019;Van Dam et al, 2019;Zhang et al, 2019). This technique is particularly useful when working with rare or geographically isolated species represented only by dried specimens in museum collections that would be difficult to collect as fresh specimens.…”

Section: Introductionmentioning

confidence: 99%

A phylogenomic tree inferred with an inexpensive PCR‐generated probe kit resolves higher‐level relationships among Neptis butterflies (Nymphalidae: Limenitidinae)

Zhang

Lohman

et al. 2020

Systematic Entomology

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Recent advances in obtaining reduced representation libraries for next‐generation sequencing permit phylogenomic analysis of species‐rich, recently diverged taxa. In this study, we performed sequence capture with homemade PCR‐generated probes to study diversification among closely related species in a large insect genus to examine the utility of this method. We reconstructed the phylogeny of Neptis Fabricius, a large and poorly studied nymphalid butterfly genus distributed throughout the Old World. We inferred relationships among 108 Neptis samples using 89 loci totaling up to 84 519 bp per specimen. Our taxon sample focused on Palearctic, Oriental and Australasian species, but included 8 African species and outgroups from 5 related genera. Maximum likelihood and Bayesian analyses yielded identical trees with full support for almost all nodes. We confirmed that Neptis is not monophyletic because Lasippa heliodore (Fabricius) and Phaedyma amphion (Linnaeus) are nested within the genus, and we redefine species groups for Neptis found outside of Africa. The statistical support of our results demonstrates that the probe set we employed is useful for inferring phylogenetic relationships among Neptis species and likely has great value for intrageneric phylogenetic reconstruction of Lepidoptera. Based on our results, we revise the following two taxa: Neptis heliodore comb. rev. and Neptis amphion comb. rev.

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Advancing mite phylogenomics: Designing ultraconserved elements for Acari phylogeny

Cited by 39 publications

References 70 publications

Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida

Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida

Sequence capture phylogenomics of historical ethanol‐preserved museum specimens: Unlocking the rest of the vault

A phylogenomic tree inferred with an inexpensive PCR‐generated probe kit resolves higher‐level relationships among Neptis butterflies (Nymphalidae: Limenitidinae)

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