Learning and Inference in Computational and Systems Biology

Detecting Evolutionary Inter-Gene Heterogeneity in Borrelia burgdorferi

author:Elisa Loza Reyes, Department of Mathematical Sciences, University of Bath
published: April 16, 2009, recorded: April 2009, views: 267

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Slides

Slides
0:00	Detecting Evolutionary Inter-Gene Heterogeneity in Borrelia burgdorferi
0:30	Contents - 1
0:36	Contents - 2
0:42	Contents - 3
0:47	Contents - 4
0:56	Phylogenetic likelihood methods - 1
1:10	Phylogenetic likelihood methods - 2
1:23	The homogeneous model
1:47	Model parameters - 1
1:52	Model parameters - 2
2:01	Model parameters - 3
2:17	Model parameters - 4
2:58	DNA data may be not homogeneous - 1
3:15	DNA data may be not homogeneous - 2
3:25	DNA data may be not homogeneous - 3
3:38	DNA data may be not homogeneous - 4
3:42	Borrelia burgdorferi - 1
4:04	Borrelia burgdorferi - 2
4:19	Borrelia burgdorferi - 3
4:23	Identification of B. burgdorferi strains - 1
5:22	Identification of B. burgdorferi strains - 2
5:27	Identification of B. burgdorferi strains - 3
5:42	Are the loci congruent in evolution, such that valid inferences can be made under a homogeneous phylogenetic model?
6:43	The Q+t mixture model - 1
7:02	The Q+t mixture model - 2
7:03	The Q+t mixture model - 3
7:07	The Q+t mixture model - 4
7:16	The Q+t mixture model - 5
7:42	A branch-length mixture model - 1
8:01	A branch-length mixture model - 2
8:30	A branch-length mixture model - 3
8:34	A branch-length mixture model - 4
8:39	A branch-length mixture model - 5
9:12	The Q+t mixture model - 6
9:42	The Q+t mixture model - 7
10:01	The Q+t mixture model - 8
10:13	The Q+t mixture model - 9
10:29	The Q+t mixture model - 10
10:31	The Q+t mixture model - 11
10:33	The Q+t mixture model - 12
10:44	The Q+t mixture model - 13
10:47	The Q+t mixture model - 14
10:50	The Q + tmixture model: an example - 1
10:57	The Q + tmixture model: an example - 2
11:06	The Q + tmixture model: an example - 3
11:07	The Q + tmixture model: an example - 4
11:09	The Q + tmixture model: an example - 5
11:11	The Q + tmixture model: an example - 6
11:12	The Q + tmixture model: an example - 7
11:13	The Q + tmixture model: an example - 8
11:15	The Q + tmixture model: an example - 9
11:21	The Q + tmixture model: an example - 10
11:35	The Q + tmixture model: an example - 11
11:42	Analysis of B. burgdorferi: the ‘housekeeping genes’ alignment - 1
11:55	Analysis of B. burgdorferi: the ‘housekeeping genes’ alignment - 2
12:19	Analysis of B. burgdorferi: the ‘housekeeping genes’ alignment - 3
12:25	Analysis of B. burgdorferi: the ‘housekeeping genes’ alignment - 4
12:26	Analysis of B. burgdorferi: the ‘housekeeping genes’ alignment - 5
12:27	Analysis of B. burgdorferi: the ‘housekeeping genes’ alignment - 6
12:30	Analysis of B. burgdorferi: the ‘housekeeping genes’ alignment - 7
12:45	Analysis of B. burgdorferi: the ‘housekeeping genes’ alignment - 8
13:33	Analysis of B. burgdorferi: the ‘housekeeping genes’ alignment - 9
13:40	Analysis of B. burgdorferi: the ‘housekeeping genes’ alignment - 10
13:45	Analysis of B. burgdorferi: the ‘housekeeping genes’ alignment - 11
13:55	Analysis of B. burgdorferi: the ‘housekeeping g.\|ospC’ alignment - 1
14:05	Analysis of B. burgdorferi: the ‘housekeeping g.\|ospC’ alignment - 2
14:11	Analysis of B. burgdorferi: the ‘housekeeping g.\|ospC’ alignment - 3
14:14	Analysis of B. burgdorferi: the ‘housekeeping g.\|ospC’ alignment - 4
14:31	Analysis of B. burgdorferi: the ‘housekeeping g.\|ospC’ alignment - 5
14:33	Analysis of B. burgdorferi: the ‘housekeeping g.\|ospC’ alignment - 6
14:54	Analysis of B. burgdorferi: the ‘housekeeping g.\|ospC’ alignment - 7
15:03	Analysis of B. burgdorferi: the ‘housekeeping g.\|ospC’ alignment - 8
15:08	Analysis of B. burgdorferi: the ‘housekeeping g.\|ospC’ alignment - 9
15:17	Conclusions - 1
15:28	Conclusions - 2
15:53	Conclusions - 3
16:13	Conclusions - 4
16:25	Conclusions - 5
16:32	- Questions

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Description

Borrelia burgdorferi is one of the bacterial species responsible for the most prevalent vector-borne disease in the temperate zone of the northern hemisphere, Lyme borreliosis [1]. Phylogenetic analyses of B. burgdorferi are now based on a concatenation of several housekeeping genes that are assumed to evolve according to one evolutionary pattern.

This is a strong assumption and, when untrue, inferences are a compromise between different phylogenetic signals., We have designed a Bayesian mixture model under a missing data formulation to automatically recover the evolutionary pattern of each site in a DNA alignment. Evolutionary consistency among a set of genes can be argued whenever most of the sites are allocated to the same evolutionary class.

Only in this case will a concatenation of genes produce valid inferences., In this study we demonstrate consistency in the evolution of eight housekeeping genes and evolutionary inconsistency between these housekeeping genes and the gene encoding the immunodominant outer surface protein C. Our method is a suitable indicator of evolutionary agreement or disagreement when employing large-scale gene concatenations, not only in B. burgdorferi, but for any phylogenetic analysis.,

[1] Margos, G. et al., 2008. Proceedings of the National Academy of Sciences of the USA, 105(25): 8730 - 8735.