1. mtActinopterygii: Analysing evolution of mitogenomes belonging to the most dominant class of vertebrates
Sevgi Kaynar1, Esra Mine Ünal1, Tuğçe Aygen1, Emre Keskin1
1 Evolutionary Genetics Laboratory (eGL),
Department of Fisheries and Aquaculture, Agricultural Faculty, Ankara University, Ankara, Turkey
Mitochondrial DNA data has widely been used for phylogenetic and population genetic analyses and becomes a potential tool in our understanding of vertebrate evolution regarding its properties such as maternal inheritance, low effective population size, lack of recombination and high evolutionary rates compared to the nuclear DNA. The main complication underlying in mitochondrial analyses are mostly based on substitution rates of the extreme variations among different sites and difficulties in estimation of pairwise distance related with parallel mutations, which makes phylogenetic inferences controversial. In order to enhance the basic information gathered from mitochondrial DNA studies of vertebrate evolution, we focused on the global mtDNA diversity in Actinopterygii (ray-finned fishes) which is known as the most dominant class of vertebrates compromising nearly 99% of fish species. Thirteen protein coding genes and two ribosomal RNA genes of 348 families with diverse origins were analysed to provide a concurrent view on vertebrate evolution.
mitochondria & actinopterygii § INTRODUCTION
analysing the mitochondrial genome § METHODS
Sequences from 2 ribosomal RNA’s and 13 protein coding genes were used to construct the phylogenetic tree of the Actinopterygii. Sequences for all genes for species assigned to the class Actinopterygii were downloaded from Genbank (accessed June 2016). Sequences for all genes were aligned using the MAFFT v1.3 Biomatters Ltd plugin in Geneious v Sequences were used to build a linked gene tree in BEAST v The appropriate nucleotide substitution model for each gene was determined using jModeltest v2.1.4, using Akaike information criterion model selection. Incomplete sampling was accounted for by a state-dependent sampling factor. We performed model simplification with MuSSE in a maximum likelihood framework based on likelihood ratio tests. We verified these results using MuSSE and our MCC tree. MuSSE allows us to associate changes in speciation with multiple character states and has been developed to incorporate the effects of incomplete taxonomic sampling. MuSSE was implemented using the R package Diversitree. Phylogenetic and statistical analyses were conducted using MEGA 7.
results from phylogenetic and statistical analyses § Table 1
12S rRNA
16S rRNA
ND1
ND2
COI
COII
ATP8
ATP6
COIII
ND3
ND4L
ND4
ND5
ND6
CYTB
Average base pairs
950
1688
959
1046
1552
691
168
684
785
349
297
1381
1837
522
1141
Conserved*
232/1493
372/2929
200/1071
120/1156
559/1911
86/979
29/301
96/748
247/792
72/360
34/303
211/1476
113/2154
61/763
275/1180
Variable*
1147/1493
2134/2929
770/1071
1008/1156
1344/1911
678/979
216/301
612/748
541/792
282/360
263/303
1199/1476
2001/2154
644/763
886/1180
Parsimony informative*
921/1493
1740/2929
680/1071
891/1156
934/1911
514/979
181/301
547/748
480/792
248/360
244/303
1065/1476
1746/2154
516/763
775/1180 T 21
21.3
28.1
25.6
29.7
27.4 26
29.3
27.9
30.8
28.3
27.6
27.3
15.3
29.1 C
26.1
24.7 31
33.4
26.9
31.2
31.1
32.9
30.4
30.2 33
30.3 A
33.8
25.4 25
28.7
31.3
25.2
22.7
23.1
27.1
28.5
38.2 G
21.8
20.2
15.5
13.1
18.4
16.4
11.5
13.4
17.3
15.4
15.7
14.9
13.9
13.5
15.2 GC
47.9
44.9
46.5
45.3
43.8
42.7
44.6 47
48.6
44.1
45.5 si
105
191
131
159
182 90 28 98 91 54 42
200
269 82
152 sv 74
164
124
194
144 69 30 80 49
206
283 97
138
R=si/sv
1.4
1.2
1.1
0.8
1.3
0.9 1
Substitution Model
GTR+G+I
(TN93+G+I)
GTR+G+I (TN93+G)
GTR+G+I (TN93+G+I)
GTR+G (TN93+G+I)
TN93+G+I (GTR+G+I)
GTR+G+I (HKY+G+I)
GTR+G (HKY+G+I)
Pairwise Distance
0.148
0.169
0.415
0.624
0.302
0.386
0.728
0.539
0.325
0.523
0.492
0.505
0.627
0.64
0.409
Standard Error
0.013
0.008
0.021
0.035
0.027
0.034
0.188
0.037
0.026
0.055
0.043
0.023
0.044
0.053
0.019
Total Major Insertions 23 7 2 24 3 6 5 11
Total Major Deletions 58 57 32 50 4 16 52 48
Max In+Del per Single Species 15
Porichthys myriaster
1+25
Tetrabrachium ocellatum
0+28
Triacanthus biaculeatus
10+10
Trichomycterus areolatus
10+11
Acanthurus leucosternon
5+10
Zu cristatus
0+14
P. myriaster
T. biaculeatus
A. leucosternon
T. areolatus
T. ocellatum
Z. cristatus
Size of the mitogenomes show a great deal of variance from base pairs (Drepaneids; Drepane punctata) to base pairs (Protanguillidae; Protanguilla palau) long. Most conserved regions were found out to be 12S and 16S rRNA with a genetic distance of and for respectively. Cytochrome c oxidase I gene of the four armed frogfish from Tetrabrachiidae family consist 28 major deletions which is highly unexpected for this region known as the barcoding gene. Detailed results of analysed genes were given in Table 1 and phylogenetic patterns were given in Figure 1. The main difference between different levels of pairwise distance could be correlated with the evolutionary mutation rate of the genes; in which protein coding 13 genes found to be much more diverse than two ribosomal RNA’s. The main nucleotide substitution model calculated for the most (14/15) of the genes was General Time Reversible. Non-uniformity of evolutionary rates among sites may be modelled by using a discrete Gamma distribution (+G) and by assuming that a certain fraction of sites are evolutionarily invariable (+I). ATP8 was calculated as the most diversified gene among specimens but this is mainly biased towards having a short (168 bp) nucleotide sequence. Dispersion patterns pointing out a more stable structure in cytochrome oxidase genes, especially in COI which is known as DNA barcode region in animals because of this attribute. Species with the highest number of InDel’s are known to be so called «ancient» species and this occurrence could be synchronised with their molecular clock.
evolution of the ray-finned fishes § RESULTS & DISCUSSION
ND2
12S rRNA
16S rRNA
ND1
COII
ATP8
ATP6
COI
COIII
ND4
ND5
ND3
ND4L
ND6
CYTB
Diversification patterns of phylogenetic trees derived from mitochondrial genome § Figure 1