The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets
Open accessAbstract
The ongoing generation of prodigious amounts of genomic sequence data from myriad vertebrates is providing unparalleled opportunities for establishing definitive phylogenetic relationships among species. The size and complexities of such comparative sequence data sets not only allow smaller and more difficult branches to be resolved but also present unique challenges, including large computational requirements and the negative consequences of systematic biases. To explore these issues and to clarify the phylogenetic relationships among mammals, we have analyzed a large data set of over 60 megabase pairs (Mb) of high-quality genomic sequence, which we generated from 41 mammals and 3 other vertebrates. All sequences are orthologous to a 1.9-Mb region of the human genome that encompasses the cystic fibrosis transmembrane conductance regulator gene (CFTR). To understand the characteristics and challenges associated with phylogenetic analyses of such a large data set, we partitioned the sequence data in several ways and utilized maximum likelihood, maximum parsimony, and Neighbor-Joining algorithms, implemented in parallel on Linux clusters. These studies yielded well-supported phylogenetic trees, largely confirming other recent molecular phylogenetic analyses. Our results provide support for rooting the placental mammal tree between Atlantogenata (Xenarthra and Afrotheria) and Boreoeutheria (Euarchontoglires and Laurasiatheria), illustrate the difficulty in resolving some branches even with large amounts of data (e.g., in the case of Laurasiatheria), and demonstrate the valuable role that very large comparative sequence data sets can play in refining our understanding of the evolutionary relationships of vertebrates.
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Cites
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582
Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference
Shimodaira, H., & Hasegawa, M. (1999) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026201 · Cited by 4,237
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971 · cited 3×
“These annotations reflect conserved elements that were detected using phastCons (Siepel et al. 2005), which applies a 2-state conserved versus nonconserved phylogenetic hidden Markov model to a 17-species multisequence alignment.”
MethodGoodman, M., Porter, C. A., Czelusniak, J., Page, S. L., Schneider, H., Shoshani, J., Gunnell, G., & Groves, C. P. (1998) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.1998.0495 · Cited by 743
Molecular evidence from retroposons that whales form a clade within even-toed ungulates
Shimamura, M., Yasue, H., Ohshima, K., Abe, H., Kato, H., Kishiro, T., Goto, M., Munechika, I., & Okada, N. (1997) · Nature · doi:10.1038/41759 · Cited by 399 · cited 1×
“…inferences based on genomic characters that change less frequently than individual nucleotides, such as inversions, transposon insertions, and coding insertions/deletions (indels) (Shimamura et al. 1997; Murphy et al. 2004, 2007; Bashir et al. 2005; Chaisson et al. 2006; Kriegs et al. 2006).”
BackgroundPhilippe, H., Delsuc, F., Brinkmann, H., & Lartillot, N. (2005) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev.ecolsys.35.112202.130205 · Cited by 306
Phylogenetic relationships and divergence times among New World monkeys (Platyrrhini, Primates).
Opazo, J. C., Wildman, D. E., Prychitko, T., Johnson, R. M., & Goodman, M. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2005.11.015 · Cited by 181
Poux, C., & Douzery, E. J. P. (2004) · American Journal of Physical Anthropology · doi:10.1002/ajpa.10322 · Cited by 103 · cited 1×
“These results largely agree with other recently reported molecular phylogenies for the primates (Barroso et al. 1997; Goodman et al. 1998; Poux and Douzery 2004; Ray et al. 2005; Opazo et al. 2006), with the exception of the relationships within Cebidae (marmoset, squirrel monkey, and owl monkey)…”
Result
Cited by
Constraints on the timescale of animal evolutionary history
Benton, M., Donoghue, P., Vinther, J., Asher, R., Friedman, M., & Near, T. (2015) · Palaeontologia Electronica · doi:10.26879/424 · Cited by 284
Mammal madness: is the mammal tree of life not yet resolved?
Foley, N. M., Springer, M. S., & Teeling, E. C. (2016) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2015.0140 · Cited by 264
Heterogeneous Models Place the Root of the Placental Mammal Phylogeny
Morgan, C. C., Foster, P. G., Webb, A. E., Pisani, D., McInerney, J. O., & O’Connell, M. J. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst117 · Cited by 123
Metadata
- Authors
- Prasad, A. B., Allard, M. W., Program, N. C. S., & Green, E. D.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2008-05-02
- Volume
- 25
- Issue
- 9
- Pages
- 1795-1808
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2051254500
- Cited by
- 235
- References
- 8
- FWCI
- 26.51
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Prasad, A. B., Allard, M. W., Program, N. C. S., & Green, E. D. (2008). Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets. Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msn104
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