When outgroups fail; Phylogenomics of rooting the emerging pathogen, Coxiella burnetii
Talima Pearson, Heidie M. Hornstra, Jason W. Sahl, Sarah Schaack, James M. Schupp, Stephen M. Beckstrom-Sternberg, Matthew W. O'Neill, Rachael A. Priestley, Mia D. Champion, James S. Beckstrom-Sternberg, Gilbert J. Kersh, James E. Samuel, Robert F. Massung, Paul Keim
Rooting phylogenies is critical for understanding evolution, yet the importance, intricacies and difficulties of rooting are often overlooked. For rooting, polymorphic characters among the group of interest (ingroup) must be compared to those of a relative (outgroup) that diverged before the last common ancestor (LCA) of the ingroup. Problems arise if an outgroup does not exist, is unknown, or is so distant that few characters are shared, in which case duplicated genes originating before the LCA can be used as proxy outgroups to root diverse phylogenies. Here, we describe a genome-wide expansion of this technique that can be used to solve problems at the other end of the evolutionary scale: where ingroup individuals are all very closely related to each other, but the next closest relative is very distant. We used shared orthologous single nucleotide polymorphisms (SNPs) from 10 whole genome sequences of Coxiella burnetii, the causative agent of Q fever in humans, to create a robust, but unrooted phylogeny. To maximize the number of characters informative about the rooting, we searched entire genomes for polymorphic duplicated regions where orthologs of each paralog could be identified so that the paralogs could be used to root the tree. Recent radiations, such as those of emerging pathogens, often pose rooting challenges due to a lack of ingroup variation and large genomic differences with known outgroups. Using a phylogenomic approach, we created a robust, rooted phylogeny for C. burnetii. [Coxiella burnetii; paralog SNPs; pathogen evolution; phylogeny; recent radiation; root; rooting using duplicated genes.]
Systematic Biology
https://doi.org/10.1093/sysbio/syt038
10.1093/sysbio/syt038
Dive into the research topics of 'When outgroups fail; Phylogenomics of rooting the emerging pathogen, Coxiella burnetii'. Together they form a unique fingerprint.
Coxiella burnetii Medicine & Life Sciences 100%
rooting Earth & Environmental Sciences 86%
Phylogeny Medicine & Life Sciences 84%
pathogen Earth & Environmental Sciences 65%
phylogeny Earth & Environmental Sciences 57%
pathogens Agriculture & Biology 41%
genome Earth & Environmental Sciences 32%
common ancestry Earth & Environmental Sciences 28%
Pearson, T., Hornstra, H. M., Sahl, J. W., Schaack, S., Schupp, J. M., Beckstrom-Sternberg, S. M., O'Neill, M. W., Priestley, R. A., Champion, M. D., Beckstrom-Sternberg, J. S., Kersh, G. J., Samuel, J. E., Massung, R. F., & Keim, P. (2013). When outgroups fail; Phylogenomics of rooting the emerging pathogen, Coxiella burnetii. Systematic Biology, 62(5), 752-762. https://doi.org/10.1093/sysbio/syt038
When outgroups fail; Phylogenomics of rooting the emerging pathogen, Coxiella burnetii. / Pearson, Talima; Hornstra, Heidie M.; Sahl, Jason W. et al.
In: Systematic Biology, Vol. 62, No. 5, 09.2013, p. 752-762.
Pearson, T, Hornstra, HM, Sahl, JW, Schaack, S, Schupp, JM, Beckstrom-Sternberg, SM, O'Neill, MW, Priestley, RA, Champion, MD, Beckstrom-Sternberg, JS, Kersh, GJ, Samuel, JE, Massung, RF & Keim, P 2013, 'When outgroups fail; Phylogenomics of rooting the emerging pathogen, Coxiella burnetii', Systematic Biology, vol. 62, no. 5, pp. 752-762. https://doi.org/10.1093/sysbio/syt038
Pearson T, Hornstra HM, Sahl JW, Schaack S, Schupp JM, Beckstrom-Sternberg SM et al. When outgroups fail; Phylogenomics of rooting the emerging pathogen, Coxiella burnetii. Systematic Biology. 2013 Sep;62(5):752-762. doi: 10.1093/sysbio/syt038
Pearson, Talima ; Hornstra, Heidie M. ; Sahl, Jason W. et al. / When outgroups fail; Phylogenomics of rooting the emerging pathogen, Coxiella burnetii. In: Systematic Biology. 2013 ; Vol. 62, No. 5. pp. 752-762.
@article{c3e17531407a43c4ada76c6c1466d46d,
title = "When outgroups fail; Phylogenomics of rooting the emerging pathogen, Coxiella burnetii",
abstract = "Rooting phylogenies is critical for understanding evolution, yet the importance, intricacies and difficulties of rooting are often overlooked. For rooting, polymorphic characters among the group of interest (ingroup) must be compared to those of a relative (outgroup) that diverged before the last common ancestor (LCA) of the ingroup. Problems arise if an outgroup does not exist, is unknown, or is so distant that few characters are shared, in which case duplicated genes originating before the LCA can be used as proxy outgroups to root diverse phylogenies. Here, we describe a genome-wide expansion of this technique that can be used to solve problems at the other end of the evolutionary scale: where ingroup individuals are all very closely related to each other, but the next closest relative is very distant. We used shared orthologous single nucleotide polymorphisms (SNPs) from 10 whole genome sequences of Coxiella burnetii, the causative agent of Q fever in humans, to create a robust, but unrooted phylogeny. To maximize the number of characters informative about the rooting, we searched entire genomes for polymorphic duplicated regions where orthologs of each paralog could be identified so that the paralogs could be used to root the tree. Recent radiations, such as those of emerging pathogens, often pose rooting challenges due to a lack of ingroup variation and large genomic differences with known outgroups. Using a phylogenomic approach, we created a robust, rooted phylogeny for C. burnetii. [Coxiella burnetii; paralog SNPs; pathogen evolution; phylogeny; recent radiation; root; rooting using duplicated genes.]",
author = "Talima Pearson and Hornstra, {Heidie M.} and Sahl, {Jason W.} and Sarah Schaack and Schupp, {James M.} and Beckstrom-Sternberg, {Stephen M.} and O'Neill, {Matthew W.} and Priestley, {Rachael A.} and Champion, {Mia D.} and Beckstrom-Sternberg, {James S.} and Kersh, {Gilbert J.} and Samuel, {James E.} and Massung, {Robert F.} and Paul Keim",
note = "Funding Information: FUNDING This work was supported by the Department of Homeland Security [HSHQDC-10-C-00139].",
doi = "10.1093/sysbio/syt038",
journal = "Systematic Biology",
T1 - When outgroups fail; Phylogenomics of rooting the emerging pathogen, Coxiella burnetii
AU - Pearson, Talima
AU - Hornstra, Heidie M.
AU - Sahl, Jason W.
AU - Schaack, Sarah
AU - Schupp, James M.
AU - Beckstrom-Sternberg, Stephen M.
AU - O'Neill, Matthew W.
AU - Priestley, Rachael A.
AU - Champion, Mia D.
AU - Beckstrom-Sternberg, James S.
AU - Kersh, Gilbert J.
AU - Samuel, James E.
AU - Massung, Robert F.
AU - Keim, Paul
N1 - Funding Information: FUNDING This work was supported by the Department of Homeland Security [HSHQDC-10-C-00139].
N2 - Rooting phylogenies is critical for understanding evolution, yet the importance, intricacies and difficulties of rooting are often overlooked. For rooting, polymorphic characters among the group of interest (ingroup) must be compared to those of a relative (outgroup) that diverged before the last common ancestor (LCA) of the ingroup. Problems arise if an outgroup does not exist, is unknown, or is so distant that few characters are shared, in which case duplicated genes originating before the LCA can be used as proxy outgroups to root diverse phylogenies. Here, we describe a genome-wide expansion of this technique that can be used to solve problems at the other end of the evolutionary scale: where ingroup individuals are all very closely related to each other, but the next closest relative is very distant. We used shared orthologous single nucleotide polymorphisms (SNPs) from 10 whole genome sequences of Coxiella burnetii, the causative agent of Q fever in humans, to create a robust, but unrooted phylogeny. To maximize the number of characters informative about the rooting, we searched entire genomes for polymorphic duplicated regions where orthologs of each paralog could be identified so that the paralogs could be used to root the tree. Recent radiations, such as those of emerging pathogens, often pose rooting challenges due to a lack of ingroup variation and large genomic differences with known outgroups. Using a phylogenomic approach, we created a robust, rooted phylogeny for C. burnetii. [Coxiella burnetii; paralog SNPs; pathogen evolution; phylogeny; recent radiation; root; rooting using duplicated genes.]
AB - Rooting phylogenies is critical for understanding evolution, yet the importance, intricacies and difficulties of rooting are often overlooked. For rooting, polymorphic characters among the group of interest (ingroup) must be compared to those of a relative (outgroup) that diverged before the last common ancestor (LCA) of the ingroup. Problems arise if an outgroup does not exist, is unknown, or is so distant that few characters are shared, in which case duplicated genes originating before the LCA can be used as proxy outgroups to root diverse phylogenies. Here, we describe a genome-wide expansion of this technique that can be used to solve problems at the other end of the evolutionary scale: where ingroup individuals are all very closely related to each other, but the next closest relative is very distant. We used shared orthologous single nucleotide polymorphisms (SNPs) from 10 whole genome sequences of Coxiella burnetii, the causative agent of Q fever in humans, to create a robust, but unrooted phylogeny. To maximize the number of characters informative about the rooting, we searched entire genomes for polymorphic duplicated regions where orthologs of each paralog could be identified so that the paralogs could be used to root the tree. Recent radiations, such as those of emerging pathogens, often pose rooting challenges due to a lack of ingroup variation and large genomic differences with known outgroups. Using a phylogenomic approach, we created a robust, rooted phylogeny for C. burnetii. [Coxiella burnetii; paralog SNPs; pathogen evolution; phylogeny; recent radiation; root; rooting using duplicated genes.]
U2 - 10.1093/sysbio/syt038
DO - 10.1093/sysbio/syt038
JO - Systematic Biology
JF - Systematic Biology