Download Response to Nelson-Sathi et al. (Nature 517, 77-80

Response to Nelson-Sathi et al. (Nature 517, 77-80)
Origins of major archaeal clades do not correspond to gene
acquisitions from bacteria
Mathieu Groussin1 , Bastien Boussau2,3,4 , Gergely J. Szöllősi5 , Laura Eme6 , Manolo Gouy2,3,4 ,
Céline Brochier-Armanet2,3,4 , Vincent Daubin2,3,4
1
– Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA,
USA
2
3
4
– Université Lyon 1, 69622 Villeurbanne, France
– CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, France
5
6
– Université de Lyon, 69361 Lyon, France
– ELTE-MTA “Lendület” Biophysics Research Group, Pázmány, Budapest, Hungary
– Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry
and Molecular Biology, Dalhousie University, Halifax, Canada
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b)
5
+ +
+
+
+ + + + + +
+ +
2
4
6
8
10
10
+
8
2
1
2
+
3
4
+
5
6
+
7
2
4
+
+
6
+
+
+
8
Maximum Likelihood
expectations (Total = 25)
25
10
15
20
+
+
+
+ +
4
+ +
+
6
+ + + +
8
10
+ + +
12
14
10
200
Nelson-Sathi et al.
estimates (Total = 1047)
+
+ + +++++
+
++++++ ++++ + +
5
Number of genomes in which the family is found
Maximum Likelihood
expectations (Total = 215)
100
150
+
50
Number of gene families inferred at the root
+
+
10
Haloarchaea
0
150
100
Maximum Likelihood
expectations (Total = 15)
50
0
Number of gene families inferred at the root
+
8
Nelson-Sathi et al.
estimates (Total = 100)
f)
Nelson-Sathi et al.
estimates (Total = 338)
+
6
+
Number of genomes in which the family is found
Methanosarcinales
+
+
Methanococcales
2
8
Number of genomes in which the family is found
e)
+
5
0
Number of gene families inferred at the root
70
60
50
40
30
20
10
+
+
0
Number of gene families inferred at the root
Maximum Likelihood
expectations (Total = 23)
+
+
+
4
d)
Nelson-Sathi et al.
estimates (Total = 128)
+
+
Number of genomes in which the family is found
Methanobacteriales
+
+
+
+
12
Number of genomes in which the family is found
c)
Maximum Likelihood
expectations (Total = 4)
6
10
Maximum Likelihood
expectations (Total = 5)
Nelson-Sathi et al.
estimates (Total = 40)
4
+
Desulfurococcales
2
Number of gene families inferred at the root
15
Nelson-Sathi et al.
estimates (Total = 59)
0
Thermoproteales
0
Number of gene families inferred at the root
a)
10
15
+
20
Number of genomes in which the family is found
Figure 1: Family size and gene gains for the “import” set at the origin of archaeal phyla.
The 6 phyla for which Nelson-Sathi et al. (2015) [NS] claim a strong signal for HGTs from bacteria at
their origins are shown. NS estimates are represented in purple. Maximum Likelihood expectations of
gains at the origin for the same datasets are represented by red crosses. Expectations of gains were
calculated from branch-specific rates of gene gain and loss estimated from the 25,762 gene families of
NS, but we report only the results for the 2,264 genes from the “import” set of NS. Most of the families
inferred to be gained at the origin of each phylum by NS are distributed over 2 or 3 archaeal genomes
only. ML estimates show that only a small fraction of gene families were actually acquired at the origin
of each phylum.
2
1000
800
Parsimony estimates
200
400
600
Maximum Likelihood estimates
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0
Number of gene gains at the origin of archaeal phyla
Nelson-Sathi et al. estimates
Figure 2: Consistency of gene family ancestral gain estimations on the “import” gene set.
Along the archaeal reference tree provided by Nelson-Sathi et al. (2015) [NS], both Parsimony (green)
and Maximum Likelihood (blue) inferences of ancestral gains were computed with Count (Csurs and
Miklos, 2006; Csurs, 2010), and compared with the estimates of NS. Wagner parsimony with a large
range of gain/loss costs combinations were tested, yielding similar estimations. Here are represented
the results with a gain cost of 2 and 4, from left to right respectively. In ML, ancestral branch-specific
gain expectations were computed from rates of gene gain and loss estimated either from the 2,264, 3,315
or 25,762 gene family sets defined by NS, from left to right respectively. All analyses are consistent and
strongly contradict the scenario of massive gene acquisitions among these 2,264 families at the origin
of archaeal phyla, claimed by NS
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References
Csurs M. 2010. Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood.
Bioinformatics 26:1910–1912.
Csurs M and Miklos I. 2006. A probabilistic model for gene content evolution with duplication, loss,
and horizontal transfer. In Proceedings of the Tenth Annual International Conference on Research in
Computational Molecular Biology (RECOMB) Vol. 3909 of Springer Lecture Notes in Bioinformatics,
Heidelberg:206–220.
Nelson-Sathi S, Sousa FL, Roettger M, Lozada-Chvez N, Thiergart T, Janssen A, Bryant D, Landan
G, Schnheit P, Siebers B, McInerney JO, and Martin WF. 2015. Origins of major archaeal clades
correspond to gene acquisitions from bacteria. Nature 517:77–80.
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