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Positive selection and biological traits related to substitution rates in mitochondrial
genes in cyprinids (Teleostei: Cyprinidae)
Abstract
Mitochondriaplayscritical rolein energy metabolism and thermoregulation for organisms.
Increasing findings suggest that natural selection acts on the mitochondrial genes and
biological traits influence rate of mitochondrial molecular evolution. Cyprinid fishes, forming
the largest family of freshwater fish in the world, exhibit great diversity in living condition
and biological traits. Thus, to analyse the evolution of mitochondrial genes and correlations of
life history traits with substitution rates in mitochondrial genes of Cyprinidae species could
provide a useful model and a reference for molecular evolution of mitochondrial genomes
(mitogenomes) of vertebrates. In the present study, the substitution rates in a total of
!mitogenomes,including threemitogenomes that we se"uenced, of species or subspecies in
family Cyprinidae were analy#ed and the correlations of substitution rates with some
biological traits of cyprinids were investigated. The results showed that (i) based on the
concatenated nucleic acid se"uences of all $! mitochondrial protein%coding genes (&C's), the
principal phylogenetic branches coincide with the taxonomy of Cyprinidae, (ii)nucleotide
substitution rates exhibited clade%specific feature, and nonsynonymous substitution rate
(dN)showed to be gene%specific, but synonymous substitution rate (dS) were fairly uniform
among $!&C's in family Cyprinidae,(iii) five main biological traits, particularly maximum
absolute fecundity, are negatively significantly correlated with the substitution rates of
mitochondrial genes, which were "uite different from other vertebrates,( )signs of positive
selection were identified along four internal branches leading to the clade of Cyprininae,
anionini, 'obionini and euciscini, and the estimated divergence time indicated these
positive selections occurred *!+ Myr % $ Myr ago.-evertheless, the results provided more
molecular information for the evolution of mitochondrial - in family Cyprinidae.
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Key words/ mitochondrial protein%coding genes0 positive selection0 biological traits0
fecundity0 substitution rate0 evolution
Introduction
Cyprinidae, the largest family of fish, comprises about ++1 genera and about +,2+1 species
with widespread distributions across 3urasia, frica and -orth merica (-elson, +114).
Many of these species are the critical sources for food (e.g., the common carp, Cyprinus
carpio), or serve as model organisms for research such as the #ebrafish, (Danio rerio)
(Mayden et al., +115). Meanwhile, all of these species are fundamental elements in the
various biotic communities in fresh waters. 6ecause of a great variety of species, morphology,
niches and food habits, the family Cyprinidae is thought to be an ideal group for studying the
molecular evolution of mitochondrial genomes (mitogenomes) of vertebrates.
Many efforts have been made to understand the evolution of cyprinid fishes based on
morphological or anatomical characters and molecular data (e.g.7owes $55$0 Chen et al.
$5820 Chen et al. $5580'illes et al. $5580 iu and Chen +11!0 9ang et al. +11).
Mitochondrial - (mt-),as a type of nearly neutral molecular mar:er, played an
important role in reconstructing the phylogenetic relationship within the family Cyprinidae
(iu and Chen +11!0 9ang et al. +110Mayden et al. +1150 Tang et al +1$1), on account of
ease in - manipulation, rapid mutation rate, lac: of significant recombination, and
availability of universal primers for - amplification (vise $5520 Morit# et al. $580
;imon et al. $552). 7owever, with more and more information available, the
interrelationships inferred from mitochondrial mar:ers and nuclear loci exhibit some
incongruence in some cyprinid groups(e.g. &erea et al. +1$10 Mayden et al. +1150 Tao et al.
+1$1). Meanwhile, increasing findings suggest that mitochondrial genes commonly show
departures from neutral evolution (6allard and 9hitloc: +1120 6lier et al. +11$0 al#iel et al.
+1140 6rown +1180 ;hen et al.+1150 ;un et al. +1$$). nd substitution rates of mitochondrial
genes can be affected by certain species characteristics including biological traits such as
body si#e and longevity (9elch et al. +1180 6romham +11+0 -unn and ;tanley $558), or
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ecological factors such as geographic niches (;un et al. +1$$0iu et al. +1$+). espite the
predominance of negative selection against deleterious mutations acting on protein%coding
mitochondrialgenes (&C's), a number of evidences suggested that there exists positive
selection as the mitochondrial evolution (e.g.p to now,
whether the correlation between biological traits and mitochondrial evolution exists and how
the positive selection of mitochondrial evolution is, to our :nowledge, are still not
investigated elaborately in cyprinids.
In order to clarify the above issues and provide a relatively panoramic view of the
evolution of &C's in cyprinids, we compared then ucleotide substitution rates of $! &C'son
mitochondrial genomes (mitogenomes) of ! cyprinid fishes, including threemitogenomes
that we se"uenced, and studied the correlations of substitution rates with five biological traits,
as well as the possibility of positive selection acting on mitochondrial genes of these clades.
Material and Methods
Three mitogenomes sequencing
To enrich the information of mitogenomes of genus Megalobrama of Cyprinidae,
mitogenomes of three breams, Megalobrama skolkovii,Megalobrama terminalis,
andMegalobrama pellegrini, were se"uenced. M.skolkovii and M. terminalis were sampled
from the &earl =iver drainage, and M. pellegriniwas collected from ongxi =iver on the
upper reaches of the
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had been were deposited in the 'en6an: with accession numbers from of @A+2++8 to
@A+2+!1.
Source of data and primary treatment
3xcept the ! mitogenomes we se"uenced, the mitogenomes for other 1 fish species or
subspecies in family Cyprinidae were downloaded from 'en6an: and 36I (available in @uly+1$+). Information on life history traits for cyprinid species was collected from Bish base
(Broese and &auly +115) and literature sources. The accession numbers of mitogenome
se"uences and the available life history traits were listed in Table ;+.
Phylogenetic analysis
Concatenated nucleic acid se"uences of all $! &C's were used to reconstruct a maximum
li:elihood (M) phylogenetic tree for cyprinids by using =xM 9eb%servers (;tamata:is et
al. +118). Myxocyprinus asiaticus (Cypriniformes/ Catostomidae) and Misgurnus
anguillicaudatus (Cypriniformes/ Cobitidae) were used as outgroups. 7owever, before
constructing M tree, Modeltest !. (&osada and Crandall $558) was used to select the best
model of evolution for subse"uent M analysis.
6ayesian analyses (M=.6
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phylogenetic tree using the codon%based Model $ (freeDratios for branches) implemented in
&M (
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lineages, and a li:elihood ratio test (=T) was constructed by comparing a model that allows
positive selection on the foreground lineages with a model that did not allow such positive
selection (Ehang et al. +11). 9hen positively selected sites were detected, &M will
identify these sites using 6ayes empirical 6ayes (636) approach to calculate posterior
probabilities (
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was used as the wor:ing topology in the subse"uent analyses as Tincayielded the low degree
of support in the M tree and the ambiguous taxonomicstatusin previous studies(9ang et al.
+110 Tang et al. +1$1).
Substitution rate variation among protein-coding mitochondrial genes in Cyprinidae
ThedS and dNvalues of all $! &'Cs along the terminal branches in cyprinids ranged from
1.11$$to $.28, and from 1to 1.1288, respectively. The average values of dSwerefrom
(AT!) to $!2 times (C"#$) of dN among different genes. The dNdS values of all $! &'Cs
along the terminal branches in cyprinids are lower than $, which indicates the genes were
under purifying selection or negative selection. Three genes of the cytochrome oxidase (CFA
or complex IG),C%T& of ubi"uinoneHcytochrome c oxidoreductase(complex III), andND'(
of -7 dehydrogenase (- or complex I) were turned out to be slow%evolving with lower
dN and dNdS values, whereas most of - genes and two T& synthase (B1B$%T&ase or
complex G)genes were classified as fast%evolving genes with higher dNand dNdS(Big.+).>%test
results further confirmed that significant difference exists in dN and dNdSbetween most of
mitochondrial &'Cs and the combined se"uences of mitochondrial genes for three complexes
(complex I, IG and G) (Table ;!).-o significant difference in dS was found among $!
individual &C's or among the ! complexes between clades although the mean values of dS
varied. The absence of divergence indicates thatthe synonymous rate is fairly uniform over
the &C's in cyprinids.
Pattern of substitution rate variation among the six clades of Cyprinidae
mong the six clades, Aenocypridini was involved in the maority of those pairwise
comparisons with significant difference, and exhibited considerably lower substitution rates in
most of the analy#ed genes and concatenated se"uences than other clades, particularly the
clades of anionini and 'obionini, (Big.+0 Table;!). Meanwhile, significant divergences in
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some &C's or combined se"uences were also detected between anionini and the clade of
Cyprininae, 'obionini and anionini, and euciscini and anionini, as well as 'obionini and
cheilognathini. 7owever, no significant divergence was found between euciscini and other
three clades, i.e. cheilognathini, 'obionini and the clade of Cyprininae. cheilognathini
showed no significant differences in dS between other five clades(Table ;!).Burthermore,
significant divergences in dNdSbetween clades of cyprinids were only found in 2 genes
(ND'(,C"# $$, C"# $$$ andAT!), two complexes (complex IG and complex G) and the
concatenated se"uence of all $! &C's (Table ;!). The clade of Aenocypridini still exhibited
pronounced difference from other clades except the clade of Cyprininae, and its mean dNdS
values were obviously lower than other clades (Big.+). dditionally, 'obionini also showed
much more significant differences from some other clades. 6ut no sign of significant
divergence in dNdSwas found in the pairwise comparisons among euciscini, cheilognathini
and the clade of Cyprininae.
dditionally, considering the difference in divergence time of clades in family Cyprinidae,
the absolute substitution rates (substitution rate per codon per million years) of the six clades
in Cyprinidae were also compared. The results were "uite similar to those from the relative
substitution rates described above (shown in Table ;!).
Positive selection analysis
The four clades of Cyprininae, anionini, 'obionini, and euciscini, respectively, hadhave
experienced significant positive selection, while various amounts of putative positively
selective sites were identified along these four internal branches (Table $).long the four
internal branches in the phylogenetic tree, positive selection has been detected in C"#$$,
C%T& andND). The divergent time estimates suggest the positive selections have occurred
during the period from the Fligocene to the middle of Miocene(from *!+ Mry ago to $ Myr
ago) (Big.$).
;trong positive selection were also identified at sites in C"# $$(++7, 2
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(branch 6 in Big.$0 Table $). Meanwhile, significant adaptive selection was also found in
branch C leading to 'obionini in ND) and in branch (euciscini). Fne site under
significant positive selection was tested inND)(+8) along branch C and in C%T&($58;)
along branch , respectively(Table $0 Big.$). -o positive selection and site under positive
selection were identified along the branches leading to cheilognathini (branch ' in Big.$)
and Aenocypridini (branch 7 in Big.$).
mong the seven sites under strong adaptive selection in CFAII of the branch 6, three sites
(7is++, Tyr2, and Gal$) were located at CFAII transmembrane domain, and other four sites
were on the periplasmic domain according to the information from &fam. These sites in the
extant species of anionini are "uite different from those in their ancestor lineage.
The uni"ue site under positive selection (;+58) in C
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Correlations of substitution rates with life history traits
The single variable regressions showed that all five biological traits, especially maximum
absolute fecundity exhibited significantly negative correlation with both d-and d; (Table +0
Big.;$). 7owever, only maximum absolute fecundity showed higher d-d; (p 1.1) in
Cyprinids whereas no significant correlations with d-d;were identified for other four
predictor traits(p 1.1). Burthermore, a multiple regression analysis including all five
biological traits also showed that only maximum absolute fecundity remained significant (dN/
n L $+, slope L %1.11+!2!, =+ L 1.282!, p L 1.1$$50 dS/ n L $+, slope L %1.121, =+L
1.!54,p L 1.1!5+5).
!iscussion
Mitochondria are the power plant of cells, which generate adenosine triphosphate (T&) for
energy%consuming processes and produce more heat for organisms in cold climates by
oxidative phosphorylation (FA&7F;) (=ui#%&esini et al. +1120 ;un et al. +1$1). The $!
peptides encoded by vertebrate mitochondrial genome are essential subunits of en#ymes in
FA&7F;. ;everal reports showed evidence of purifying selection and the physiological or
functional constraints on mt- evolution (6allard and 9hitloc: +1120 Mei:leohn et al.
+110 ;hen et al. +1150 ;un et al. +1$1). Thus, in the present study, we analy#ed the evolution
of &'Cs based on the genome information from ! species or subspecies in family
Cyprinidae.
&arameter dNdScan provide a measure of selective pressure at protein level. The dNdSvalue
less than $ significantly indicates that nonsynonymous mutations are deleterious and fixed in
the population at a lower rate than synonymous mutations, called purifying selection or
negative selection (i et al. $580
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phylogenetic tree, some genes (ND), C"#$$ and C%T&) have undergone positive selection.
;ome advantageous nonsynonymous mutations might retain by adaptive selection would be
enriched in internal branches relative to terminal branches (=ui#%&esini et al. +112). The
universally detected significant divergences in dNdS of terminal branches among these
mitochondrial genes indicate diverse purifying selection on mitochondrial genes. 'enes under
stronger purifying selection usually encode the subunits forming the catalytic core (e.g.C"#$,
C"#$$and C%T&) (6runori et al. $58, 7altia et al. $55$, T#u:ihara $554) or playing critical
roles in structural stability of complexes (e.g.C"#$$$andND'() (T#u:ihara $5540 ervinen
+112) in FA&7F;, whereas, genes encoding for - and T& synthase are generally under
wea:er purifying selection in cyprinids. similar trend also has been observed in avian and
other fish taxa (;hen +1150 Marsall +1150 ;un +1$1). The uniform distribution of dSamong
genes highlights that significantly different dNbetween the two groups of genes is attributed to
the pronounced divergence in dNdSin cyprinids. 6ecause of the important roles of some genes
playing in functions of FA&7F;, nonsynonymous mutations are usually deleterious, even
lethalto organisms, which were then swept by purifying selection.
ivergent time estimates suggest the positive selections, which have been detected in
C"#$$, C%T& andND),have occurred from the Fligocene to the middle of Miocene. uring
this period of time, the maor geographical events are the uplift of Tibetan plateau and the
land%sea redistributions associated with the continental collision of India and sia, which are
estimated to start from the early Ceno#oic at least ! Myr ago (n et al. +11$0 =owley and
Currie +1140 7arris +114). These geographical events are mainly attributed to the significant
continental aridification and cooling in sia (n et al. +11$0 'uo et al. +11+0'uillaume et al.
+110 =amstein et al. $55). =ecent findings suggest that C"#$$may have more important
roles for heat generation than for energy production in teleost (;un et al. +1$$).There were
studies showing that the adaptive mutations in C%T& genes are associated with the
adaptability to colder climates in humans (=ui#%&esini et al. +112). - encodes -7
dehydrogenase in mitochondria, which is shown to play an important role in proton or
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sodium ion translocation in overall respiration regulation in mammals (-a:amaru%Fgiso et al.
+11!) (6ai et al. +112).
Moreover, our results indicate the ancestral lineages of six cyprinid clades distributing in
different regions have experienced to various degrees selection pressure originating from the
abrupt changes in palaeo environmental conditions from the Fligocene to the middle of
Miocene. -o positive selection site has been detected in the branches leading to
Aenocypridini and cheilognathini and a few numbers of positively selective sites occurred in
the branches leading to euciscini and 'obionini living in high latitude while much more
selection sites involved in more genes has been found in the clades of anionini and
Cyprininae. The maority of the extant species of anionini are small%si#ed fishes inhabiting
in hilly streams and rivers, or shallow, slow%moving and standing waters such as rice paddies
and other temporally%inundated environments in southwest of China and southern sia. The
various habitats of anionini might suggest their ancestral lineages adapt to the temporary
waters caused by aridification orand swift streams or rivers attribute to the tectonic processes.
Combined the fossil records and the distributions of the extant species in the clade of
Cyprininae (6anarescu and Coad $55$0 -elson +1140 ;chul#%Mirbach and =eichenbacher,
+1140 Chen et al. $558), the main origin of the Cyprininae sensu latomight be related to the
uplift of Tibetan plateau and the continental collision of India and sia from the early
Fligocene to the early Miocene and one of the lineages of the primitive barbins could
accumulate more adaptive mutations in genes and differentiate into the extant species in latter
Cyprininae.
&resently, it has become increasingly clear that numerous aspects of its biology in
mammals, birds and reptiles affected their genome evolution (6romham +11+0 -unn and
;tanley $5580 9elch et al. +118). ;imilar to other vertebrates, life history traits, such as
lifespan and body si#e, in cyprinids have been also shown significantly negative relationships
with the rate of their mitochondrial molecular evolution in our study. 7owever, the
relationship between fecundity of cyprinid fishes and the evolutionary rates of mitochondrial
&C's are "uite different from other vertebrates. In mammals, the fecundity has strongly
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positive association with both synonymous and non%synonymous rates for six nuclear genes,
(9elch et al. +118). In reptiles, a positive correlation between clutch si#e and total genetic
distance for cytochrome bhas been found (6romham et al. +11+). In ourstudy, the fecundity
of cyprinid fishes arenot only isthe strongest predictor of mitochondrial - substitution
rate variations, but also showed significant negative relationships with both synonymous and
non%synonymous rates for the concatenated se"uence of $! mitochondrial protein%coding
genes.6romham(+1$$) mentioned that the strongly positive relationship between fecundity
and genetic variation in mammals waswereresulted from the number of genome copies per
generation scales. s we :now, hundreds of thousands of eggs of fishes are derived from a
finite amount of oogonial stem cells that can generate a new cohort of oocytes each year
('ilbert +114), yet the higher fecundity seems toplay no more roles in increasing copy error
mutations in cyprinids. Cyprinid fishes are a group of primitive teleostean that are strictly
distributed in freshwater and their living conditions including hydrological regimes, spawning
grounds,and feeding conditions, etc, fluctuate fre"uently. Moreover, the vast maority of
cyprinids practice external fertili#ation and external development of #ygotes, and the #ygotes
and the young offspring are lac: of parental protection (9eyl and 6ooth $5550 Ehang et al.
+1$$). 7ence, N%ecological or nearly N%ecological strategy with high fecundities, high
mortalities of early life stages, and young age at maturation, which adopted by the vast
maority of cyprinids (9eyl and 6ooth $555), would be another cause for the significant
negative relationships between the fecundity of cyprinid fishes with both synonymous and
non%synonymous rates.
In conclusion, the evolution of mitochondrial genes and correlations of life history traits
with substitution rates in mitochondrial genes in Cyprinidae enriched and provided a
reference for molecular evolution of mitogenomes of vertebrates. The cyprinids had have
experienced significant positive selection, which has beenweredetected in C"#$$, C%T& and
ND), while various amounts of putative positively selective sites were identified. The
relationship between fecundity of cyprinid fishes and the evolving rates of mitochondrial
&C's were significantly negative, which are"uite different from other vertebrates.
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"upporting in#ormation
Table "$mplification primers for mitogenomes of ! breams Megalobrama s:ol:ovii, M.
terminalis, and M. pellegrini.
Table "%The accession numbers of mitogenome se"uences from 'en6an: and the available
life history traitsfrom Bishbase.
Table "&The divergence in substitution rates in individual mitochondrial gene, three
complexes and the combined se"uence of the $! genes.
'ig"$Correlations of substitution rates with biological traits. , correlations of substitution
rates with Max absolute fecundity0 6,correlations of substitution rates with Max body mass0C,correlations of substitution rates with Max body length0 , correlations of substitution rates
with length at first maturity0 3, Max lifespan.
Acnowledgements
This study was supported by grants from the Modern groindustry Technology=esearch
;ystem, OO;taple Breshwater Bishery Industry Technology ;ystemPP (-o. C=;%24%
1),Bundamental =esearch Bunds for the Central >niversities (-o.
+1$$&
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6allard @9F, 9hitloc: MC. +112. The incomplete natural history of mitochondria.Mol *co.
$!/ +5H22.
6anarescu &, Coad 69. $55$. Cyprinidae of 3urasiaIn Cyprinid fishes, ;ystematics, 6iology
and 3xplotation (9infield I@ and -elson @3, eds), $st edition. ondon, Chapman and 7all/
$+H$.
6lier &>, ufresne B, 6urton =;. +11$. -atural selection and the evolution of mt-%
encoded peptides/ evidence for intergenomic co%adaptation. Trends +enet. $/ 211H214.
6romham . +11+. Molecular Cloc:s in =eptiles/ ife 7istory Influences =ate of Molecular
3volution.Mol &iol *vol. $5(!)/ !1+%!15.
6rown . +118. Bish mitochondrial genomics, se"uence, inheritance and functional
variation., -ish &iol. +/ !H!2.
6runori M, ntonini ', Malatesta B, ;arti &, 9ilson MT. $58. Cytochrome%c
oxidase.;ubunit structure and proton pumping.*ur , &iochem. $45/$H8.
Chang M, Chen &. +111. &hanero#oic succession of fish faunas in mainland China. In/ Chow
-
7/26/2019 Positive Selection and Biological Traits Related
16/26
rummond , =ambaut . +11. 63;T/ 6ayesian evolutionary analysis by sampling trees.
&MC *vol &iol. / +$2.
Broese =, &auly . +115. Bish6ase.9orld 9ide 9eb electronic publication.vailable from
www.fishbase.org, version ($$+115).
'ilbert ;B. +114. evelopmental 6iology.;underland/ ;inauer ssociates.
'illes , ecointre ', Baure 3, Chappa# =, 6run '. $558. Mitochondrial phylogeny of
3uropean cyprinids/ implications for their systematics, reticulate evolution, and
coloni#ation time.Mol hylogenet *vol. $1/ $!+H$2!.
'uillaume , rigsman 9, angereis C', bels 7, ai ;, Ban A. +11. Tibetan plateau
aridification lin:ed to global cooling at the 3oceneHFligocene transition. Nature. 22/
4!H4!8.
'uo ET, 9illiam B=, 7ao JE, 9u 76, Jiao
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i 97, 9u CI, uo CC. $58. new method for estimating synonymous and
nonsynonymous rates of nucleotide substitutions considering the relative li:elihood of
nucleotide and codon changes.Mol &iol *vol. +/$1H$2.
ittle ', ougheed ;C, Moyes C. +1$+. 3volution of mitochondrial%encoded cytochrome
oxidase subunits in endothermic fish/ the importance of taxon%sampling in codon%based
models.Mol hylogenet *vol. 4!/ 45H482
iu 7, Chen
-
7/26/2019 Positive Selection and Biological Traits Related
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i
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19/26
;chul#%Mirbach T, =eichenbacher 6. +114. =econstruction of Fligocene and -eogene
freshwater fish faunas% an actualistic study on cypriniforms otoliths.Acta aleontol ol.
$(+)/ +8!H!12.
;hen
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'igure legends
'ig $ The phylogenetic tree o# cyprinids based on $& protein*coding genes #rom
mitogenomes and molecular dating o# the +% cyprinid species or subspecies 6ootstrap
support values and 6ayesian posterior probabilities are shown at nodes and separated by
slashes for maximum li:elihood and Mrbayes, respectively.6ranch , 6, C, , ', 7 represent
the branches leading to the clades of Cyprininae, anionini, 'obionini, euciscini,
cheilognathini and Aenocypridini, respectively. 6ranch 3 and B indicate the ancestral
lineages of Cyprinini and extant genus Carassius, respectively. The fossil%based constraints
are indicated with diamonds. 6ranch lengths are proportional to divergence times (in million
of years). The names of species shadowed by gray belong to the clade of Cyprininae. The
names of species in box belong to Carassias.
'ig % Comparisons o# median and the averagevalues o# dN,dS- dNand dS#or $& individual
genes- genes involved in comple.es I- I/- and /- and $& protein*coding genes set in +%
cyprinid species among si. clades o# cyprinids6oxes include 1K of the distributions. (a)
Comparison of median and the average values ofdNdS. (b) Comparison of median and theaverage values ofdN. (c) Comparisons of median and the average values ofdS.
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Table $ Parameter estimates- lielihood ratio testsand positively selected sites under 0ranch*site ModelA test %
0ranch or
lineage
1enes Model A test % 2stimates o# parameters 3d# %3ln4 P value Positively selected sites
branch A ND3 alternative model p1 L 1.8+,p$ L 1.1!, D1L 1.122, D+L $.!$4 $ 1.1+5 p X 1.1 !!+I
null model p1 L 1.81,p$ L 1.1$, D1L 1.122,D+L $ -one
ND' alternative model p1 L 1.54, p$ L 1.1+2, D1L 1.1+!, D+L !.884 $ $.1+ pX 1.1 !5
null model p1 L 1.5,p$ L 1.1+2, D1L 1.1+!,D+L $ -one
ND) alternative model p1 L 1.84,p$ L 1.14, D1L 1.124, D+L .!1 $ +2.$8 pY 1.11$ 56, &7!, &89, !M, 2$T,
8&K, 5G, $%T, ++!, &85',7+8;, 7$M, ,
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lineage o# C"# $ alternative model p1 L 1.55$ ,p$ L1.11+ , D1L 1.11, D+L $.111 $ 1.!8+ & X 1.1 285M
Cyprinini null model p1 L 1.55$,p$ L 1.11+, D1L1.11 ,D+L $.111 -one
C"#
$$
alternative model p1 L 1.52!,p$ L 1.1$+, D1L 1.1$ , D+L$.111 $ 2.+8+ & Y 1.1 7&I
null model p1 L1.525,p$ L 1.1$!, D1L 1.1$,D+L $.111 -one
C"#
$$$
alternative model p1 L 1.51,p$L 1.1$2 ,D1L 1.1$+, D+L $.111 $ 1.!5 & X 1.1 $$
-one
null model p1 L 1.51,p$ L1.1$2, D1L 1.1$+,D+L $.111
ND5 alternative model p1 L 1.52,p$ L 1.1$8 , D1L 1.1+$,D+L $.111 $ 1.!1 & X 1.1 $=8Inull model p1 L 1.52,p$ L 1.1$8, D1L 1.1+$,D+L $.111 -one
ND3 alternative model p1 L 1.858,p$ L 1.14, D1L 1.12!,D+L $.111 $ 1.41 & X 1.1 T,%=&I,++8;,%$I,&&$/
null model p1 L 1.858,p$ L 1.14, D1L 1.12!,D+L $.111
ND' alternative model p1 L 1.541,p$ L 1.1+2, D1L 1.1++,D+L $.111 $ 1.52 & X 1.1 &84,&
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Table % "ingle variable regression analyses on substitution rates and biological traits
ates Trait n Coe##icients: slope % p*
value
dN6dS Max absolute
fecundity
+4 1.2$$ 1.$45 1.1![
Max body mass + 1.!2 1.$+ 1.1[
Max body length 41 1.$+ 1.1! 1.$8
length at first maturity +5 1.+4 1.14 1.$44
Max lifespan +$ 1.! 1.18+ 1.$$+
dN Max absolute
fecundity
+4 %1.45 1.28 1[[
Max body mass + %1.215 1.$4 1.1!2[Max body length 41 %1.2!$ 1.$84 1.1$[
length at first maturity +5 %1.248 1.+$5 1.115[
Max lifespan +$ %1.22 1.+54 1.1$$[
dS Max absolute
fecundity
+4 %1. 1.25 1[[
Max body mass + %1.2$$ 1.$45 1.1!![
Max body length 41 %1.22 1.+$+ 1[[
length at first maturity +5 %1.22$ 1.$52 1.1$[
Max lifespan +$ %1.!5 1.+5 1.1$+[ [p1.1, [[p1.11.
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'ig $ The phylogenetic tree o# cyprinids based on $& protein*coding genes #rom mitogenomes and molecular dating o# the +% cyprinid
species or subspecies 6ootstrap support values and 6ayesian posterior probabilities are shown at nodes and separated by slashes for maximum
li:elihood and Mrbayes, respectively.6ranch , 6, C, , ', 7 represent the branches leading to the clades of Cyprininae, anionini, 'obionini,euciscini, cheilognathini and Aenocypridini, respectively. 6ranch 3 and B indicate the ancestral lineages of Cyprinini and extant genusCarassius, respectively. The fossil%based constraints are indicated with diamonds. 6ranch lengths are proportional to divergence times (in millionof years). The names of species shadowed by gray belong to the clade of Cyprininae. The names of species in box belong to Carassias.
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(a)
(b)
(c)
'ig % Comparisons o# median and the averagevalues o# dN,dS- dNand dS#or $& individual
genes- genes involved in comple.es I- I/- and /- and $& protein*coding genes set in +%
cyprinid species among si. clades o# cyprinids6oxes include 1K of the distributions. (a)Comparison of median and the average values ofdNdS. (b) Comparison of median and the
average values ofdN. (c) Comparisons of median and the average values ofdS.