The relationship between the rate of molecular evolution and the rate of genome rearrangement in animal mitochondrial genomes.
Wei Xu(1), Daniel Jameson(2), Paul G Higgs(1).
(1)Department of Physics, McMaster University, Hamilton, Ontario.
(2) School of Biological Sciences, University of Manchester, UK.
Background to this project
1
3
Phylogenetic Artefacts – Gene sequences are often used in molecular phylogenetics studies to deduce the evolutionary relationship between species.
This is difficult with mitochondrial genomes because of the presence of rapidly evolving ‘problem species’ with very divergent sequences (which
leads to long branch attraction), and due to the wide variation in the frequency of bases and amino acids among species (which causes biases in trees).
Can Gene Order Help? – Gene order rearrangements sometimes provide strong evidence of shared ancestry of a group, e.g. the translocation of
tRNA-Leu shown in the Drosophila genome (see 2) is a derived character shared by many other insects and crustaceans, and this supports the
existence of the Pancrustacea clade. The gene order of Rhipicephalus is shared by two other ticks and no other species, which is a strong signature of
the relationship of this group. However, there are also species, such as Tigriopus, with extremely scrambled genomes, where gene order tells us little.
Chelicerata
Sequence Evolution and Genome Rearrangement are Related – Here we will show that species with high rates of sequence evolution also tend to
have high rates of genome rearrangement. Problem species in molecular phylogenetics also tend to be problems in gene order studies.
OGRe is a relational database for comparative analysis of mitochondrial genomes.
It contains information on gene sequences, gene order and genome rearrangements.
Please visit OGRe on-line at http://ogre.mcmaster.ca
2
4
Protein Tree
Terebratulina
Katharina
Limulus
Maximum Likelihood branch lengths were obtained using
this fixed topology. The protein tree (left) is derived from
a concatenation of 4 mitochondrial proteins. The tRNA
tree (right) is derived from a concatenation of 22
mitochondrial tRNAs. For each species, the total branch
length from the root of the arthropods (A) to the tip was
measured (see Table 1). Rates of sequence evolution vary
substantially between species.
Vargula
Hutchinsoniella
Tigriopus
Armillifer
Argulus
Tetraclita
Pollicipes
Penaeus
Cherax
Portunus
Panulirus
Pagurus
Artemia
Triops
Daphnia
Tetrodontophora
Gomphiocephalus
Tricholepidion
Locusta
Aleurodicus
Triatoma
Philaenus
Thrips
A
P
It is thought that the ancestral gene order (at A) is the
same as Limulus. Therefore, the break point and inversion
distances from Limulus to each species were measured.
Lepidopsocid
Heterodoxus
Pyrocoelia
Tribolium
Crioceris
Apis
Melipona
Limulus and the fruit fly, Drosophila, differ by a single translocation of
a tRNA-Leu gene (shown in yellow and marked by an arrow).
Ornithoctonus
Habronattus
Speleonectes
P
Heptathela
A consensus tree topology for arthropods was obtained
from morphological evidence, published molecular
phylogenies and our own analysis of mitochondrial
sequences. The base of the pancrustacea (P) was left as a
multifurcation as there is no reliable consensus.
Scutigera
Lithobius
Thyropygus
Narceus
A
Limulus
Methods
Heptathela
Ornithoctonus
Habronattus
Varroa
Carios
Ornithodoros moubata
Ornithodoros porcinus
Rhipicephalus
Amblyomma
Haemaphysalis
Ixodes holocyclus
Ixodes hexagonus
Ixodes persulcatus
Typical animal mitochondrial genomes contain 13 protein-coding genes, 2 rRNAs
and 22 tRNAs. OGRe produces comparisons of mitochondrial gene orders for any
two species. The examples below show comparisons between the Horseshoe crab,
Limulus polyphemus and three other arthropods. These genomes a circular – the
two ends are connected – but they are shown as linear for convenience. Each gene
is shown as a block labelled by its gene symbol. Single letter abbreviations are for
tRNA genes. Genes drawn below the central line are transcribed from left to right.
Genes drawn above the line are transcribed from right to left (and a – sign is added
to the gene symbol).
tRNA Tree
Terebratulina
Katharina
Ostrinia
Antheraea
Bombyx
Anopheles
Drosophila
Chrysomya
Myriapoda
Tigriopus
Armillifer
Argulus
Tetraclita
Pollicipes
Penaeus
Cherax
Portunus
Panulirus
Pagurus
Artemia
Triops
Daphnia
Tetrodontophora
Gomphiocephalus
Tricholepidion
Locusta
Aleurodicus
Triatoma
Philaenus
Crustacea
Thrips
Lepidopsocid
Heterodoxus
Pyrocoelia
Tribolium
Crioceris
Apis
Melipona
Ostrinia
Antheraea
Bombyx
Anopheles
Drosophila
Chrysomya
5
0.1
Varroa
Carios
Ornithodoros moubata
Ornithodoros porcinus
Rhipicephalus
Amblyomma
Haemaphysalis
Ixodes holocyclus
Ixodes hexagonus
Ixodes persulcatus
Scutigera
Lithobius
Thyropygus
Narceus
Speleonectes
Vargula
Hutchinsoniella
Hexapoda
0.1
Results
Limulus polyphemus
the Horseshoe crab
Limulus and the tick, Rhipicephalus, differ by several gene
rearrangements, but many common stretches of identical gene order are
found between the two species (as indicated by the colour scheme). A
point of discontinuity of gene order between two species is called a
break point. The Break Point Distance between two species is the
number of break points (7 in this example). This is the simplest
quantitative measure of the amount of genome rearrangement that has a
occurred. Another measure is the Inversion Distance, i.e. the minimum
number of inversions of DNA sections that would be required to
convert one gene order into the other. Limulus can be converted to
Rhipicephalus with 6 inversions. This does not imply that inversion is
the dominant mechanism of genome rearrangement. Translocations and
duplication/deletion processes can rearrange gene orders without
changing strands. Only tRNA-Cys has changed strand in this case.
Image courtesy of Marine Biology
Laboratory, Woods Hole.
www.mbl.edu/animals/Limulus
Breakpoints Inversions
Tigriopus
japonicus
35
32
Heterodoxus
macropus
35
32
Thrips
imaginis
32
29
Pollicipes
polymerus
22
16
Cherax
destructor
20
16
Tetraclita
japonica
20
16
Argulus
americanus
20
18
Speleonectes
tulumensis
19
16
Apis
mellifera
19
16
Hutchinsoniella
macracantha
18
16
Pagurus
longicarpus
18
12
Vargula
hilgendorfii
17
15
Lepidopsocid
RS-2001
17
16
Habronattus
oregonensis
16
14
Ornithoctonus
huwena
15
13
Scutigera
coleoptrata
15
15
Melipona
bicolor
14
8
Varroa
destructor
14
12
Armillifer
armillatus
13
12
Narceus
annularus
9
9
Thyropygus
sp.
9
9
Aleurodicus
dugesii
8
5
Anopheles
gambiae
8
6
Tetrodontophora bielanensis
8
6
Artemia
franciscana
7
5
Rhipicephalus
sanguineus
7
6
Amblyomma
triguttatum
7
6
Haemaphysalis
flava
7
6
Locusta
migratoria
6
5
Bombyx
mori
6
5
Portunus
trituberculatus
6
5
Ostrinia
furnacalis
6
5
Tribolium
castaneum
6
5
Antheraea
pernyi
6
5
Chrysomya
putoria
4
2
Tricholepidion
gertschi
3
2
Daphnia
pulex
3
2
Pyrocoelia
rufa
3
2
Drosophila
melanogaster
3
2
Panulirus
japonicus
3
2
Triatoma
dimidiata
3
2
Lithobius
forficatus
3
3
Philaenus
spumarius
3
2
Gomphiocephalus hodgsoni
3
2
Penaeus
monodon
3
2
Crioceris
duodecimpunctata
3
2
Triops
cancriformis
3
2
Limulus
polyphemus
0
0
Ixodes
persulcatus
0
0
Ixodes
holocyclus
0
0
Ixodes
hexagonus
0
0
Carios
capensis
0
0
Ornithodoros
porcinus
0
0
Heptathela
hangzhouensis
0
0
Ornithodoros
moubata
0
0
Dup/Del
0
0
1
2
0
0
0
1
0
0
0
0
0
0
0
0
2
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
tRNA
2.15
1.39
1.34
0.69
0.54
0.66
0.72
0.83
0.84
0.86
0.65
0.79
0.60
1.48
1.95
0.48
0.93
0.83
0.85
0.63
0.49
1.04
0.41
0.77
0.63
0.82
0.88
0.82
0.38
0.51
0.51
0.49
0.55
0.50
0.36
0.44
0.62
0.52
0.37
0.58
0.59
1.13
0.69
0.69
0.34
0.55
0.42
0.36
0.72
0.76
0.74
0.70
0.67
0.76
0.68
Protein
1.34
1.83
1.32
0.59
0.57
0.57
1.12
0.93
1.50
0.87
0.45
1.41
0.59
1.09
1.23
0.44
1.66
1.09
1.73
0.58
0.46
1.54
0.47
0.70
0.64
0.96
1.00
0.96
0.52
0.54
0.44
0.48
0.53
0.54
0.42
0.39
0.51
0.77
0.42
0.53
0.50
0.61
0.58
0.62
0.32
0.58
0.40
0.40
0.82
0.83
0.90
0.79
0.86
0.87
0.88
Table 1
The gene order of the crustacean Tigriopus is completely scrambled
with respect to Limulus. There are 35 break points for only 37 genes.
The Limulus order has features in common with non-arthropod species,
and is thought to be the ancestral arthropod gene order. The Tigriopus
gene order has very little in common with any other known species.
Thus there has been extensive recent genome scrambling in this lineage.
Breakpoint category
Very High
High
Moderate
Low
min
1.33
0.48
0.38
0.34
tRNA distance
mean
1.62
0.86
0.63
0.60
only tRNA High
only tRNA Mod/Low
0.66
0.34
1.01
0.60
Table 2
max
2.14
1.94
1.04
1.13
min
1.32
0.44
0.43
0.32
1.94
1.13
0.57
0.32
Table 1 shows the two gene-order distances and the two
sequence-based distances between the ancestral
arthropod and each current species. The number of
deleted or duplicated genes with respect to the ancestor is
also shown. Species are classed into four categories
according to breakpoint distance (shown by colour).
r = 0.59
Images coutesy of University of Nebraska,
Dept.of Entomology.
http://entomology.unl.edu/images/
This is also demonstrated by Table 2, which shows the
minimum, mean and maximum of the sequence-based
distances in each of the categories. Species with high
break point distances also have high tRNA and protein
distances.
It is found that tRNA genes are more frequently
translocated than rRNA or protein genes. There are many
species where only tRNAs have moved. This includes 9
species whose breakpoint distance is in the ‘High’
category and 21 species in the ‘Moderate’ or ‘Low’
break point categories. In Table 2, the two bottom rows
show that, even when only tRNAs have moved, there are
higher tRNA and protein distances for species with
higher breakpoint distances. This means that high rates
of tRNA translocation are correlated with increased rate
of evolution in tRNA and protein genes.
protein distance
mean
max
1.50
1.83
0.99
1.73
0.69
1.54
0.62
0.90
1.15
0.63
r = 0.99
The figure on the right shows that all four distance
measures are positively correlated with each other. The
correlation coefficients are shown by each graph.
1.73
1.54
Acknowledgements
r = 0.53
r = 0.69
This work is supported by Canada
Research Chairs and NSERC.
Discussion
These results show that the rates of both sequence evolution and genome rearrangement are very nonclocklike. Species with high evolutionary rates often have close relatives with much lower rates. This
means that rates have increased in scattered lineages independently. For example:
Holometabolous insects :
Bees (Apis, Melipona) >> Beetles (Tribolium, Crioceris)
Hemiptera (bugs) :
Aleurodicus >> Triatoma
Maxillopod crustaceans :
Tigriopus, Argulus >> Tetraclita, Pollicipes
Spiders :
Ornithoctonus, Habronattus >> Heptathela
This suggests a breakdown in accuracy of mitochondrial genome replication in the fast-evolving
lineages that causes higher mutation rate and higher susceptibility to major rearrangements, but it is
also possible to envisage selective explanations, such as rapid adaptation to a new environment.
There are still many questions that we do not understand. Why do tRNAs move much more frequently
than larger genes? Why are there many examples of ‘long jump’ translocations of tRNAs? Why are
there many examples of genes whose positions are reshuffled but remain on the same strand (no
inversions)? We hope that further analysis of the OGRe gene order database will give some clues to
these questions.