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1.
Prehistoric Introduction of Domestic Pigs onto the Okinawa Islands: Ancient Mitochondrial DNA Evidence 总被引:3,自引:0,他引:3
Watanobe T Ishiguro N Nakano M Takamiya H Matsui A Hongo H 《Journal of molecular evolution》2002,55(2):222-231
Ancient DNAs of Sus scrofa specimens excavated from archaeological sites on the Okinawa islands were examined to clarify the genetic relationships among
prehistoric Sus scrofa, modern wild boars and domestic pigs inhabiting the Ryukyu archipelago, the Japanese islands, and the Asian continent. We
extracted remain DNA from 161 bone specimens excavated from 12 archaeological sites on the Okinawa islands and successfully
amplified mitochondrial DNA control region fragments from 33 of 161 specimens. Pairwise difference between prehistoric and
modern S. scrofa nucleotide sequences showed that haplotypes of the East Asian domestic pig lineage were found from archaeological specimens
together with Ryukyu wild boars native to the Ryukyu archipelago. Phylogenetic analysis of 14 ancient sequences (11 haplotypes;
574 bp) indicated that S. scrofa specimens from two Yayoi-Heian sites (Kitahara and Ara shellmiddens) and two Recent Times sites (Wakuta Kiln and Kiyuna sites)
are grouped with modern East Asian domestic pigs. Sus scrofa specimens from Shimizu shellmidden (Yayoi-Heian Period) were very closely related to modern Sus scrofa riukiuanus but had a unique nucleotide insertion, indicating that the population is genetically distinct from the lineage of modern
Ryukyu wild boars. This genetic evidence suggests that domestic pigs from the Asian continent were introduced to the Okinawa
islands in the early Yayoi-Heian period (1700–2000 BP), or earlier. 相似文献
2.
The complete mitochondrial genome sequence of the pig, Sus scrofa, was determined. The length of the sequence presented is 16,679 nucleotides. This figure is not absolute, however, due to
pronounced heteroplasmy caused by variable numbers of the motif GTACACGTGC in the control region of different molecules. A
phylogenetic study was performed on the concatenated amino acid and nucleotide sequences of 12 protein-coding genes of the
mitochondrial genome. The analysis identified the pig (Suiformes) as a sister group of a cow/whale clade, making Artiodactyla
paraphyletic. The split between pig and cow/whale was molecularly dated at 65 million years before present.
Received: 2 December 1997 / Accepted: 20 February 1998 相似文献
3.
A Phylogenetic Study of the Origin of the Domestic Pig Estimated from the Near-Complete mtDNA Genome 总被引:18,自引:0,他引:18
The near-complete pig mtDNA genome sequence (15,997 bp) was determined from two domestic pigs (one Chinese Meishan and one
Swedish Landrace) and two European wild boars. The sequences were analyzed together with a previously published sequence representing
a Swedish domestic pig. The sequences formed three distinct clades, denoted A, E1, and E2, with considerable sequence divergence
between them (0.8–1.2%). The results confirm our previous study (based on the sequence of the cytochrome B gene and the control
region only) and provide compelling evidence that domestication of pigs must have occurred from both an Asian and a European
subspecies of the wild boar. We estimated the time since the divergence of clade A (found in Chinese Meishan pigs) and E1
(found in European domestic pigs) at about 900,000 years before present, long before domestication about 9000 years ago. The
pattern of nucleotide substitutions among the sequences was in good agreement with previous interspecific comparisons of mammalian
mtDNA; the lowest substitution rates were observed at nonsynonymous sites in protein-coding genes, in the tRNA and rRNA genes,
while the highest rates were observed at synonymous sites and in the control region. The presence of Asian clade A in some
major European breeds (Large White and Landrace) most likely reflects the documented introgression of Asian germplasm into
European stocks during the 18th and 19th centuries. The coexistence of such divergent mtDNA haplotypes for 100+ generations
is expected to lead to the presence of recombinant haplotypes if paternal transmission and recombination occur at a low frequency.
We found no evidence of such recombination events in the limited sample studied so far.
Received: 19 April 2000; Accepted: 15 November 2000 相似文献
4.
5.
Mitochondrial DNA Sequence and Phylogenetic Evaluation of Geographically Disparate Sus scrofa Breeds
M. V. Cannon T. D. Brandebourg M. C. Kohn D. Đikić M. H. Irwin 《Animal biotechnology》2013,24(1):17-28
Next generation sequencing of mitochondrial DNA (mtDNA) facilitates studies into the metabolic characteristics of production animals and their relation to production traits. Sequence analysis of mtDNA from pure-bred swine with highly disparate production characteristics (Mangalica Blonde, Mangalica Swallow-bellied, Meishan, Turopolje, and Yorkshire) was initiated to evaluate the influence of mtDNA polymorphisms on mitochondrial function. Herein, we report the complete mtDNA sequences of five Sus scrofa breeds and evaluate their position within the phylogeny of domestic swine. Phenotypic traits of Yorkshire, Mangalica Blonde, and Swallow-belly swine are presented to demonstrate their metabolic characteristics. Our data support the division of European and Asian breeds noted previously and confirm European ancestry of Mangalica and Turopolje breeds. Furthermore, mtDNA differences between breeds suggest function-altering changes in proteins involved in oxidative phosphorylation such as ATP synthase 6 (MT-ATP6), cytochrome oxidase I (MT-CO1), cytochrome oxidase III (MT-CO3), and cytochrome b (MT-CYB), supporting the hypothesis that mtDNA polymorphisms contribute to differences in metabolic traits between swine breeds. Our sequence data form the basis for future research into the roles of mtDNA in determining production traits in domestic animals. Additionally, such studies should provide insight into how mtDNA haplotype influences the extreme adiposity observed in Mangalica breeds. 相似文献
6.
Characterization and Evolution of the Mitochondrial DNA Control Region in Hornbills (Bucerotiformes)
We determined the mitochondrial DNA control region sequences of six Bucerotiformes. Hornbills have the typical avian gene
order and their control region is similar to other avian control regions in that it is partitioned into three domains: two
variable domains that flank a central conserved domain. Two characteristics of the hornbill control region sequence differ
from that of other birds. First, domain I is AT rich as opposed to AC rich, and second, the control region is approximately
500 bp longer than that of other birds. Both these deviations from typical avian control region sequence are explainable on
the basis of repeat motifs in domain I of the hornbill control region. The repeat motifs probably originated from a duplication
of CSB-1 as has been determined in chicken, quail, and snowgoose. Furthermore, the hornbill repeat motifs probably arose before
the divergence of hornbills from each other but after the divergence of hornbills from other avian taxa. The mitochondrial
control region of hornbills is suitable for both phylogenetic and population studies, with domains I and II probably more
suited to population and phylogenetic analyses, respectively. 相似文献
7.
Evolutionary geneticists have increasingly used sequence variation in mitochondrial DNA (mtDNA) as a source of historical
information. However, conclusions based on these data remain tentative because a sufficiently clear understanding of the evolutionary
dynamics of mtDNA has yet to be developed. In this paper we present the results of computer simulations designed to illustrate
the effects of social structure, geographical structure, and population size on the rate of nucleotide substitution and lineage
sorting of mtDNA. The model is based in part on the social structure of macaque monkeys. Simulated populations of females
were divided into 25 social groups; the animals in each were distributed in a hierarchy of four dominance rank categories.
The probabilities for offspring survivorship were varied among dominance ranks to reflect the fitness consequences of social
structure. Population size was varied across runs from 100 to 300 females. The pattern of female migration was also varied
to mimic either the island model or the stepping-stone model. All these variables are shown to affect the lineage sorting
period (LSP), and certain combinations of parameter values can cause the retention of mtDNA polymorphisms for a very long
time. In addition, the simulations exhibited a negative relationship between the LSP and substitution rate over a modest and
realistic range of LSP values. An important implication of these results is that estimates of time since isolation based on
the assumption of a constant molecular clock may be biased and unreliable. 相似文献
8.
Christiane Delarbre Ann-Sofie Rasmussen Ulfur Arnason Gabriel Gachelin 《Journal of molecular evolution》2001,53(6):634-641
The complete sequence of the mitochondrial DNA of the hagfish Myxine glutinosa has been determined. The hagfish mtDNA (18,909 bp) is the longest vertebrate mtDNA determined so far. The gene arrangement
conforms to the consensus vertebrate type and differs from that of lampreys. The exceptionally long (3628-bp) control region
of the hagfish contains the typical conserved elements found in other vertebrate mtDNAs but is characterized by a large number
of putative hairpins, which can potentially fold into a highly compact secondary structure that appears to be unique to hagfish.
The comparison of the mtDNAs of two M. glutinosa specimens, excluding the control region, shows a 0.6% divergence at the nucleotide level as a sample of intraspecies polymorphism.
Received: 21 August 2000 / Accepted: 2 March 2001 相似文献
9.
Here we report DNA sequences from mitochondrial cytochrome b gene segments (1,005 base pairs per species) for the extinct woolly mammoth (Mammuthus primigenius) and Steller's sea cow (Hydrodamalis gigas) and the extant Asian elephant (Elephas maximus), the Western Indian manatee (Trichechus manatus), and the hyrax (Procavia capensis). These molecular data have allowed us to construct the phylogeny for the Tethytheria. Our molecular data resolve the trichotomy
between the two species of living elephants and the mammoth and confirm that the mammoth was more closely related to the Asian
elephant than to the African elephant. Our data also suggest that the sea cow–dugong divergence was likely as ancient as the
dugong–manatee split, and it appears to have been much earlier (22 million years ago) than had been previously estimated (4–8
million years ago) by immunological comparison.
Received: 8 August 1996 / Accepted: 30 September 1996 相似文献
10.
The complete mitochondrial DNA, mtDNA, molecule of the greater rhea, Rhea americana, was sequenced. The size of the molecule is 16,710 nucleotides. The organization of the molecule conforms with that described
for the chicken and the ostrich. It has been shown previously that relative to other vertebrates the NADH3 gene of the ostrich
has an insertion of one nucleotide in position 174 of the gene. The same observation was made in the rhea and in the newly
sequenced NADH3 gene of the emu, Dromaius novaehollandiae. Comparison with the NADH3 gene of the chicken and the rook suggests that the inserted nucleotide may be deleted by RNA editing.
The divergence between the two struthioniform species, the ostrich and the rhea, was molecularly dated at ≈51 million years
before present, MYBP. This dating is more recent than commonly acknowledged. Phylogenetic analysis of the complete cytochrome
b genes of seven avian orders placed the Passeriformes basal in the avian tree with the Struthioniformes among the remaining
Neognathae. These findings challenge the commonly accepted notion that the most basal avian divergence is that between the
Palaeognathae and Neognathae.
Received: 13 October 1997 / Accepted: 17 January 1998 相似文献
11.
Miyuki Noro Ryuichi Masuda Irena A. Dubrovo Michihiro C. Yoshida Makoto Kato 《Journal of molecular evolution》1998,46(3):314-326
Complete sequences of cytochrome b (1,137 bases) and 12S ribosomal RNA (961 bases) genes in mitochondrial DNA were successfully determined from the woolly mammoth
(Mammuthus primigenius), African elephant (Loxodonta africana), and Asian elephant (Elephas maximus). From these sequence data, phylogenetic relationships among three genera were examined. Molecular phylogenetic trees reconstructed
by the neighbor-joining and the maximum parsimony methods provided an identical topology both for cytochrome b and 12S rRNA genes. These results support the ``Mammuthus-Loxodonta' clade, which is contrary to some previous morphological reports that Mammuthus is more closely related to Elephas than to Loxodonta.
Received: 8 April 1997 / Accepted: 23 July 1997 相似文献
12.
Eduardo Eizirik Sandro L. Bonatto Warren E. Johnson Peter G. Crawshaw Jr. Jean Cristophe Vié Dulce M. Brousset Stephen J. O'Brien Francisco M. Salzano 《Journal of molecular evolution》1998,47(5):613-624
The ocelot (Leopardus pardalis) and margay (L. wiedii) are sister-species of Neotropical cats which evolved from a lineage that migrated into South America during the formation
of the Panamanian land bridge 3–5 million years ago. Patterns of population genetic divergence of each species were studied
by phylogenetic analyses of mitochondrial DNA (mtDNA) control region sequences in individuals sampled across the distribution
of these taxa. Abundant genetic diversity and remarkably concordant phylogeographic partitions for both species were observed,
identifying parallel geographic regions which likely reflect historical faunal barriers. Inferred aspects of phylogeography,
population genetic structure, and demographic history were used to formulate conservation recommendations for these species.
In addition, observed patterns of sequence variation provided insight into the molecular evolution of the mtDNA control region
in closely related felids.
Received: 26 January 1998 / Accepted: 14 May 1998 相似文献
13.
Weinreich DM 《Journal of molecular evolution》2001,52(1):40-50
A higher rate of molecular evolution in rodents than in primates at synonymous sites and, to a lesser extent, at amino acid
replacement sites has been reported previously for most nuclear genes examined. Thus in these genes the average ratio of amino
acid replacement to synonymous substitution rates in rodents is lower than in primates, an observation at odds with the neutral
model of molecular evolution. Under Ohta's mildly deleterious model of molecular evolution, these observations are seen as
the consequence of the combined effects of a shorter generation time (driving a higher mutation rate) and a larger effective
population size (resulting in more effective selection against mildly deleterious mutations) in rodents. The present study
reports the results of a maximum-likelihood analysis of the ratio of amino acid replacements to synonymous substitutions for
genes encoded in mitochondrial DNA (mtDNA) in these two lineages. A similar pattern is observed: in rodents this ratio is
significantly lower than in primates, again consistent only with the mildly deleterious model. Interestingly the lineage-specific
difference is much more pronounced in mtDNA-encoded than in nuclear-encoded proteins, an observation which is shown to run
counter to expectation under Ohta's model. Finally, accepting certain fossil divergence dates, the lineage-specific difference
in amino acid replacement-to-synonymous substitution ratio in mtDNA can be partitioned and is found to be entirely the consequence
of a higher mutation rate in rodents. This conclusion is consistent with a replication-dependent model of mutation in mtDNA.
Received: 24 September 1999 / Accepted: 18 September 2000 相似文献
14.
Dorothy E. Pumo Peter S. Finamore William R. Franek Carleton J. Phillips Sima Tarzami Darlene Balzarano 《Journal of molecular evolution》1998,47(6):709-717
The complete mitochondrial genome was obtained from a microchiropteran bat, Artibeus jamaicensis. The presumptive amino acid sequence for the protein-coding genes was compared with predicted amino acid sequences from several
representatives of other mammalian orders. Data were analyzed using maximum parsimony, maximum likelihood, and neighbor joining.
All analyses placed bats as the sister group of carnivores, perissodactyls, artiodactyls, and cetaceans (e.g., 100% bootstrap
value with both maximum parsimony and neighbor joining). The data strongly support a new hypothesis about the origin of bats,
specifically a bat/ferungulate grouping. None of the analyses supported the superorder Archonta (bats, flying lemurs, primates,
and tree shrews). Our hypothesis regarding the relationship of bats to other eutherian mammals is concordant with previous
molecular studies and contrasts with hypotheses based solely on morphological criteria and an incomplete fossil record. The
A. jamaicensis mitochondrial DNA control region has a complex pattern of tandem repeats that differs from previously reported chiropteran
control regions.
Received: 22 January 1998 / Accepted: 3 June 1998 相似文献
15.
Ballard JW 《Journal of molecular evolution》2000,51(1):64-75
The current study compares the nucleotide variation among 22 complete mitochondrial genomes of the three distinct Drosophila simulans haplotypes with intron 1 of the alcohol dehydrogenase-related locus. This is the first study to investigate the sequence variation of multiple complete mitochondrial genomes within distinct
mitochondrial haplotypes of a single species. Patterns of variation suggest distinct forces are influencing the evolution
of mitochondrial DNA (mtDNA) and autosomal DNA in D. simulans. First, there is little variation within each mtDNA haplotype but strong differentiation among them. In contrast, there is
no support for differentiation of the mitochondrial haplotypes at the autosomal locus. Second, there is a significant deficiency
of mitochondrial variation in each haplotype relative to the autosomal locus. Third, the ratio of nonsynonymous to synonymous
substitutions is not equal in all branches of the well-resolved phylogeny. There is an excess of nonsynonymous substitutions
relative to synonymous substitutions within each D. simulans haplotype. This result is similar to that previously observed within the mtDNA of distinct species. A single evolutionary
force may be causally linked to the observed patterns of mtDNA variation—a rickettsia-like microorganism, Wolbachia pipientis, which is known to directly influence mitochondrial evolution but have a less direct influence on autosomal loci.
Received: 16 September 1999 / Accepted: 14 March 2000 相似文献
16.
Ballard JW 《Journal of molecular evolution》2000,51(1):48-63
In this study, a comparative genomics approach is employed to investigate the forces that shape evolutionary change in the
mitochondrial DNA (mtDNA) of members of the Drosophila melanogaster subgroup. This approach facilitates differentiation of the patterns of variation resulting from processes acting at a higher
level from those acting on a single gene. The mitochondrial genomes of three isofemale lines of D. simulans (siI, -II, and -III), two of D. melanogaster (Oregon R and a line from Zimbabwe), and D. mauritiana (maI and -II), and one of D. sechellia were sequenced and compared with that derived from D. yakuba. Data presented here indicate that at least three broad mechanisms shape the evolutionary dynamics of mtDNA in these taxa.
The first set of mechanisms is intrinsic to the molecule. Dominant processes may be interpreted as selection for an increased
rate of replication of the mtDNA molecule, biases in DNA repair, and differences in the pattern of nucleotide substitution
among strands. In the genes encoded on the major strand (62% of the coding DNA) changes to or from C predominate, whereas
on the minor changes to or from G predominate. The second set of mechanisms affects distinct lineages. There are evolutionary
rate differences among lineages, possibly owing to population demographic changes or changes in mutational biases. This is
supported by the heterogeneity found in synonymous, nonsynonymous, and silent substitutions. The third set of mechanisms differentially
affects distinct genes. A maximum-likelihood sliding-window analysis detected four disjunct regions that have a significantly
different nucleotide substitution process from that derived from the complete sequence. These data show the potential for
comparative genomics to tease apart subtle forces that shape the evolution of DNA.
Received: 30 July 1999 / Accepted: 16 March 2000 相似文献
17.
A mitochondrial DNA (mtDNA) phylogeny of cichlid fish is presented for the most taxonomically inclusive data set compiled
to date (64 taxa). 16S rDNA data establish with confidence relationships among major lineages of cichlids, with a general
pattern congruent with previous morphological studies and less inclusive molecular phylogenies based on nuclear genes. Cichlids
from Madagascar and India are the most basal groups of the family Cichlidae and sister to African–Neotropical cichlids. The
cichlid phylogeny suggests drift-vicariance events, consistent with the fragmentation of Gondwana, to explain current biogeographic
distributions. Important phylogenetic findings include the placement of the controversial genus Heterochromis basal among African cichlids, the South American genus Retroculus as the most basal taxon of the Neotropical cichlid assemblage, and the close relationship of the Neotropical genera Cichla with Astronotus rather than with the crenicichlines. Based on a large number of South American genera, the Neotropical cichlids are defined
as a monophyletic assemblage and shown to harbor significantly higher levels of genetic variation than their African counterparts.
Relative rate tests suggest that Neotropical cichlids have experienced accelerated rates of molecular evolution. But these
high evolutionary rates were significantly higher among geophagine cichlids.
Received: 18 September 1998 / Accepted: 16 December 1998 相似文献
18.
The fluvial sculpin, Cottus
nozawae, is a coldwater-adapted fish distributed in Hokkaido Island and the northeastern part of Honshu Island (Tohoku District),
Japan. Mitochondrial DNA (mtDNA) control region sequencing was used to investigate the geographic distribution of genetic
variation and phylogeography of C. nozawae. Most populations possessed unique haplotypes, few being shared across river systems. Phylogenetic analysis of the sequences
of the mtDNA control region and adjacent regions of C. nozawae revealed three distinct phylogenetic groups that differed by 3.05% to 3.11%, corresponding to distinct geographic regions,
Hokkaido Island, northern Tohoku District, and Yamagata Prefecture (southwestern Tohoku District), respectively. The divergence
times of three groups were estimated to be about 1.5 million years ago by applying a general rate for mtDNA, suggesting that
the divergence among them might have occurred in the early Pleistocene. Divergence among the haplotypes within the group from
the northern Tohoku District was also high (1.84%), no haplotypes being shared by local populations in different river systems
in this region. Local populations from a single river system in this region comprise a distinct lineage that differed from
other river systems. Such genetically divergent population structures among the different regions and river systems are considered
to have resulted mainly from long-term isolation and restricted gene flow among river systems, probably promoted by the fluvial
benthic life history and low dispersal ability of this species.
Received: April 12, 2001 / Revised: December 1, 2001 / Accepted: December 19, 2001 相似文献
19.
The complete mitochondrial DNA (mtDNA) of the donkey and mtDNA comparisons among four closely related mammalian species-pairs 总被引:7,自引:0,他引:7
The nucleotide sequence of the complete mitochondrial genome of the donkey, Equus asinus, was determined. The length of the molecule is 16,670 bp. The length, however, is not absolute due to pronounced heteroplasmy
caused by variable numbers of two types of repetitive motifs in the control region. The sequence of the repeats is (a) 5′-CACACCCA
and (b) 5′-TGCGCGCA, respectively. The order of (a) and (b) can be expressed as {n[2(a)+(b)]+m(a)}. In 32 different clones analyzed the number of n and m ranged from 0 to 9 and 1 to 7. The two rRNA genes, the 13 peptide-coding genes, and the 22 tRNA genes of the donkey and the
horse, Equus caballus, were compared in detail. Total nucleotide difference outside the control region was 6.9%. Nucleotide difference between peptide-coding
genes ranged from 6.4% to 9.4% with a mean of 8.0%. In the inferred protein sequences of the 13 peptide-coding genes the amino
acid difference was 0.2–8.8%, and the mean for the 13 concatenated amino acid sequences was 1.9%. In the 22 tRNA genes, the
mean difference was 3.5%, and that in the two rRNA genes was 4.1%. The mtDNA differences between the donkey and the horse
suggest that the evolutionary separation of the two species occurred ≈9 million years ago. Analyses of differences among the
mtDNAs of three other species-pairs, harbor seal/grey seal, fin whale/blue whale, and Homo/common chimpanzee, showed that the relative evolutionary rate of individual peptide-coding genes varies among different species-pairs
and modes of comparison. The findings show that the superimposition of sequence data of one lineage for resolving and dating
evolutionary divergences of other lineages should be performed with caution unless based on comprehensive data.
Received: 15 October 1995 / Accepted: 15 April 1996 相似文献
20.
We previously reported the sequence of a 9260-bp fragment of mitochondrial (mt) DNA of the cephalopod Loligo bleekeri [J. Sasuga et al. (1999) J. Mol. Evol. 48:692–702]. To clarify further the characteristics of Loligo mtDNA, we have sequenced an 8148-bp fragment to reveal the complete mt genome sequence. Loligo mtDNA is 17,211 bp long and possesses a standard set of metazoan mt genes. Its gene arrangement is not identical to any other
metazoan mt gene arrangement reported so far. Three of the 19 noncoding regions longer than 10 bp are 515, 507, and 509 bp
long, and their sequences are nearly identical, suggesting that multiplication of these noncoding regions occurred in an ancestral
Loligo mt genome. Comparison of the gene arrangements of Loligo, Katharina tunicata, and Littorina saxatilis mt genomes revealed that 17 tRNA genes of the Loligo mt genome are adjacent to noncoding regions. A majority (15 tRNA genes) of their counterparts is found in two tRNA gene clusters
of the Katharina mt genome. Therefore, the Loligo mt genome (17 tRNA genes) may have spread over the genome, and this may have been coupled with the multiplication of the
noncoding regions. Maximum likelihood analysis of mt protein genes supports the clade Mollusca + Annelida + Brachiopoda but
fails to infer the relationships among Katharina, Loligo, and three gastropod species.
Received: 9 May 2001 / Accepted: 3 October 2001 相似文献