The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.
Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales
Abstract
Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, non-model avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.
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Cites
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BackgroundUltraconserved Elements in the Human Genome
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Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development
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Cited by
Whole-genome analyses resolve early branches in the tree of life of modern birds
Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., Ho, S. Y. W., Faircloth, B. C., Nabholz, B., Howard, J. T., et al. (2014) · Science · doi:10.1126/science.1253451 · Cited by 1,901
Self-citationA phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes
Pyron, R., Burbrink, F. T., & Wiens, J. J. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-93 · Cited by 1,641
Phylogenetic classification of bony fishes
Betancur-R, R., Wiley, E. O., Arratia, G., Acero, A., Bailly, N., Miya, M., Lecointre, G., & Ortí, G. (2017) · BMC Evolutionary Biology · doi:10.1186/s12862-017-0958-3 · Cited by 857
Selecting optimal partitioning schemes for phylogenomic datasets
Lanfear, R., Calcott, B., Kainer, D., Mayer, C., & Stamatakis, A. (2014) · BMC Evolutionary Biology · doi:10.1186/1471-2148-14-82 · Cited by 762
Hughes, L. C., Ortí, G., Huang, Y., Sun, Y., Baldwin, C. C., Thompson, A. W., Arcila, D., Betancur-R., R., Li, C., Becker, L., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1719358115 · Cited by 575
Metadata
- Authors
- Faircloth, B. C., McCormack, J. E., Crawford, N. G., Harvey, M. G., Brumfield, R. T., & Glenn, T. C.
- Venue
- Systematic Biology
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-01-09
- Volume
- 61
- Issue
- 5
- Pages
- 717-726
- ISSN
- 1063-5157 (ISSN-L)
- 1076-836X
- OpenAlex
- W2122302865
- Cited by
- 1,270
- References
- 11
- FWCI
- 16.03
- Type
- journal article
- Language
- en
- Open access
- closed
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