High phylogenetic utility of an ultraconserved element probe set designed for Arachnida

Arachnida is an ancient, diverse and ecologically important animal group that contains a number of species of interest for medical, agricultural and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to ar...

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Bibliographic Details
Published in:Molecular ecology resources 2017-07, Vol.17 (4), p.812-823
Main Authors: Starrett, James, Derkarabetian, Shahan, Hedin, Marshal, Bryson, Robert W., McCormack, John E., Faircloth, Brant C.
Format: Article
Language:English
Subjects:
Agricultural engineering
Animals
Arachnida
Arachnida - classification
Arachnida - genetics
Arachnids
Araneae
Arthropods
Biologists
Biology
Deoxyribonucleic acid
DNA
DNA Probes
DNA sequencing
Ecology
Enrichment
Gene expression
Genetic resources
Genomes
Genomics
Loci
Markers
Opiliones
Phylogenetics
phylogenomics
Phylogeny
population genomics
Population studies
Probes
Scorpiones
Sequence Analysis, DNA
Systematics
target enrichment
ultraconserved elements
Wildlife conservation
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Summary:Arachnida is an ancient, diverse and ecologically important animal group that contains a number of species of interest for medical, agricultural and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress. Here, we present a genomic toolkit for arachnids featuring hundreds of conserved DNA regions (ultraconserved elements or UCEs) that allow targeted sequencing of any species in the arachnid tree of life. We used recently developed capture probes designed from conserved regions of available arachnid genomes to enrich a sample of loci from 32 diverse arachnids. Sequence capture returned an average of 487 UCE loci for all species, with a range from 170 to 722. Phylogenetic analysis of these UCEs produced a highly resolved arachnid tree with relationships largely consistent with recent transcriptome‐based phylogenies. We also tested the phylogenetic informativeness of UCE probes within the spider, scorpion and harvestman orders, demonstrating the utility of these markers at shallower taxonomic scales and suggesting that these loci will be useful for species‐level differences. This probe set will open the door to phylogenomic and population genomic studies across the arachnid tree of life, enabling systematics, species delimitation, species discovery and conservation of these diverse arthropods.
ISSN:1755-098X
1755-0998
DOI:10.1111/1755-0998.12621