Complete nucleotide sequence of the mitochondrial genome of a salamander, Mertensiella luschani

doi:10.1016/S0378-1119(03)00655-3

Gene

Volume 317, 23 October 2003, Pages 17-27

https://doi.org/10.1016/S0378-1119(03)00655-3 Get rights and content

Abstract

The complete nucleotide sequence (16,650 bp) of the mitochondrial genome of the salamander Mertensiella luschani (Caudata, Amphibia) was determined. This molecule conforms to the consensus vertebrate mitochondrial gene order. However, it is characterized by a long non-coding intervening sequence with two 124-bp repeats between the tRNA^Thr and tRNA^Pro genes. The new sequence data were used to reconstruct a phylogeny of jawed vertebrates. Phylogenetic analyses of all mitochondrial protein-coding genes at the amino acid level recovered a robust vertebrate tree in which lungfishes are the closest living relatives of tetrapods, salamanders and frogs are grouped together to the exclusion of caecilians (the Batrachia hypothesis) in a monophyletic amphibian clade, turtles show diapsid affinities and are placed as sister group of crocodiles+birds, and the marsupials are grouped together with monotremes and basal to placental mammals. The deduced phylogeny was used to characterize the molecular evolution of vertebrate mitochondrial proteins. Amino acid frequencies were analyzed across the main lineages of jawed vertebrates, and leucine and cysteine were found to be the most and least abundant amino acids in mitochondrial proteins, respectively. Patterns of amino acid replacements were conserved among vertebrates. Overall, cartilaginous fishes showed the least variation in amino acid frequencies and replacements. Constancy of rates of evolution among the main lineages of jawed vertebrates was rejected.

Introduction

Salamanders, the tailed amphibians (order Caudata), may represent a living paradigm of the tempo and mode in which the adaptations that are required to live on land were acquired in the evolution of vertebrates. Many of the 400 or so living salamander species (Frost, 1985) display peculiar feeding, breathing, urogenital, and reproductive apparati, which can be interpreted as alternative or sequential morphological adaptations to terrestrial life that were evolved when sarcopterygian ancestors of amphibians colonized land in the Devonian (360 MYA). Moreover, salamanders are also characterized by a wide variety of gametogenetic, mating, developmental, and parental care strategies (Duellman and Trueb, 1994), which can be perceived as an adaptation to permit reproduction on terrestrial conditions.

To trace and better understand the sequence of evolutionary events that produced the diversity in life modes exhibited by salamanders, it is mandatory first to infer the phylogenetic relationships of the group with other living amphibians (i.e. frogs and caecilians) and with other vertebrates (Titus and Larson, 1995). Therefore, we determined the complete sequence of the mitochondrial genome of an old world salamander, Mertensiella luschani. The usefulness of these new mitochondrial sequence data in resolving controversies on amphibian phylogenetic relationships was addressed elsewhere (Zardoya and Meyer, 2001). Here, we present a formal description of the molecular and structural features of the salamander mitochondrial genome and compared it with the complete mitochondrial genomes of other relevant jawed vertebrates.

Section snippets

Mitochondrial DNA extraction

Mitochondrial DNA (mtDNA) was purified from eggs and liver of six specimens of the salamander species M. luschani, as previously described (Zardoya et al., 1995). After homogenization, mitochondria were separated from intact nuclei and cellular debris by a low-speed centrifugation. Mitochondrial DNA was extracted from isolated mitochondria by a standard alkaline lysis procedure, and cleaved with EcoRI and HindIII restriction enzymes. Two EcoRI fragments of 1.3 (comprising the complete control

Organization of the salamander mitochondrial genome

The mitochondrial genome of the salamander M. luschani is 16,650 bp long and conforms to the consensus vertebrate mitochondrial gene order (Fig. 1). As in other vertebrates, 2 rRNAs, 22 tRNAs, and 13 proteins are encoded by the salamander mitochondrial genome (Fig. 1). The overall base composition of the L-strand is A: 32%, T: 29%, C: 24%, and G: 15%. There are only nine noncoding intergenic spacer nucleotides. Interestingly, this paucity of intergenic spacers contrasts with the existence of a

Acknowledgments

Meredith J. Mahoney gave very useful advice on primers and PCR conditions to amplify the salamander ND4 gene. We thank two anonymous reviewers for their useful comments on an earlier version of the paper. R.Z. was sponsored by a postdoctoral contract of the Ministerio de Educacion y Cultura of Spain. This work received partial financial support from grants from the Lion Foundation, the Deutsche Forschungs Gemeinschaft (ME 1725/4-1), the University of Konstanz, the US National Science Foundation

References (68)

P. Desjardins et al.
Sequence and gene organization of the chicken mitochondrial genome
J. Mol. Biol.
(1990)
C.D. Hurst et al.
The complete mitochondrial DNA sequence of the Atlantic salmon, Salmo salar
Gene
(1999)
M. Miya et al.
Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion
Mol. Phylogenet. Evol.
(2000)
B.A. Roe et al.
The complete nucleotide sequence of the Xenopus laevis mitochondrial genome
J. Biol. Chem.
(1985)
T.W. Wong et al.
In vitro replication of human mitochondrial DNA: accurate initiation at the origin of light-strand synthesis
Cell
(1985)
J. Adachi et al.
Model of amino acid substitution in proteins encoded by mitochondrial DNA
J. Mol. Evol.
(1996)
E. Arevalo et al.
Mitochondrial DNA sequence divergence and phylogenetic relationships among eight chromosome races of the Sceloporus grammicus complex (Phrynosomatidae) in Central Mexico
Syst. Biol.
(1994)
U. Arnason et al.
Comparison between the complete mtDNA sequences of the blue and the fin whale, two species that can hybridize in nature
J. Mol. Evol.
(1993)
Y. Cao et al.
The complete mitochondrial DNA sequence of the shark Mustelus manazo: evaluating rooting contradictions to living bony vertebrates
Mol. Biol. Evol.
(1998)
R.L. Carroll
Vertebrate Paleontology and Evolution
(1988)

J. Castresana

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

Mol. Biol. Evol.

(2000)

Y.S. Chang et al.

The complete nucleotide sequence, gene organization of carp (Cyprinus carpio) mitochondrial genome

J. Mol. Evol.

(1994)

R. Cloutier et al.

Interrelationships of basal sarcopterygians

C. Delarbre et al.

The complete nucleotide sequence of the mitochondrial DNA of the dogfish, Scyliorhinus canicula

Genetics

(1998)

J. Devereux et al.

A comprehensive set of sequence analysis programs for the VAX

Nucleic Acids Res.

(1984)

J.N. Doda et al.

Elongation of displacement loop strands in human and mouse mitochondrial DNA is arrested near specific template sequences

Proc. Natl. Acad. Sci. U. S. A.

(1981)

W.E. Duellman et al.

Biology of Amphibians

(1994)

J. Felsenstein

Confidence limits on phylogenies: an approach using the bootstrap

Evolution

(1985)

D.R.E. Frost

Amphibian Species of the World. A Taxonomic and Geographical Reference

(1985)

W.K. Gregory

The monotremes and the palimpsest theory

Bull. Am. Mus. Nat. Hist.

(1947)

A. Härlid et al.

Analyses of mitochondrial DNA nest ratite birds within the Neoagnathae: supporting a neotenous origin of ratite morphological characters

Proc. R. Soc. Lond. B

(1999)

A. Härlid et al.

The mtDNA sequence of the ostrich and the divergence between paleognathous and neognathous birds

Mol. Biol. Evol.

(1997)

S. Horai et al.

Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs

Proc. Natl. Acad. Sci. U. S. A.

(1995)

J.P. Huelsenbeck et al.

MrBayes: bayesian inference of phylogeny

Bioinformatics

(2001)

J.G. Inoue et al.

Complete mitochondrial DNA sequence of the Japanese sardine Sardinops melanostictus

Fish. Sci.

(2000)

J.G. Inoue et al.

Complete mitochondrial DNA sequence of the Japanese eel, Anguilla japonica

Fish. Sci.

(2001)

J.G. Inoue et al.

Complete mitochondrial DNA sequence of Conger myriaster (Teleostei: Anguilliformes): novel gene order for vertebrate mitochondrial genomes and the phylogenetic implications for anguilliform families

J. Mol. Evol.

(2001)

A. Janke et al.

The complete mitochondrial genome of Alligator mississipiensis and the separation between recent Archosauria (Birds and crocodiles)

Mol. Biol. Evol.

(1997)

A. Janke et al.

The marsupial mitochondrial genome and the evolution of placental mammals

Genetics

(1994)

A. Janke et al.

The mitochondrial genome of a monotreme-the platypus (Ornithorhynchus anatinus)

J. Mol. Evol.

(1996)

S. Johansen et al.

The complete mitochondrial DNA sequence of Atlantic cod, Gadus morhua: relevance to taxonomic studies among cod-fishes

Mol. Mar. Biol.

(1996)

D.T. Jones et al.

The rapid generation of mutation data matrices from protein sequences

Comp. Appl. Biosci.

(1992)

A. Kawaguchi et al.

Complete mitochondrial DNA sequence of Aulopus japonicus (Teleostei: Aulopiformes), a basal Eurypterygii: longer DNA sequences and higher-level relationships

Ichthyol. Res.

(2001)

J.K. Killian et al.

Marsupials and Eutherians reunited: genetic evidence for the Theria hypothesis of mammalian evolution

Mammal. Genome

(2001)

Cited by (29)

Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes
2014, Molecular Phylogenetics and Evolution
Citation Excerpt :
Here, we present one of the largest time-calibrated phylogenies of primates estimated using complete mitochondrial genome sequences. Mitogenomic analyses have been shown to be useful for phylogenetic reconstruction and divergence time estimation at different taxonomic levels and in different groups, including amphibians (Zardoya et al., 2003; Zhang et al., 2005; Zhang and Wake, 2009), birds (Pereira and Baker, 2006; Slack et al., 2007; Pacheco et al., 2011), fish (Inoue et al., 2003, 2010; Miya et al., 2003), and mammals (Arnason and Janke, 2002; Arnason et al., 2002, 2004, 2008). Mitochondrial genomes have traditionally been used for phylogenetic and phylogeographic analyses of animal taxa.
The origins and the divergence times of the most basal lineages within primates have been difficult to resolve mainly due to the incomplete sampling of early fossil taxa. The main source of contention is related to the discordance between molecular and fossil estimates: while there are no crown primate fossils older than 56 Ma, most molecule-based estimates extend the origins of crown primates into the Cretaceous. Here we present a comprehensive mitogenomic study of primates. We assembled 87 mammalian mitochondrial genomes, including 62 primate species representing all the families of the order. We newly sequenced eleven mitochondrial genomes, including eight Old World monkeys and three strepsirrhines. Phylogenetic analyses support a strong topology, confirming the monophyly for all the major primate clades. In contrast to previous mitogenomic studies, the positions of tarsiers and colugos relative to strepsirrhines and anthropoids are well resolved. In order to improve our understanding of how fossil calibrations affect age estimates within primates, we explore the effect of seventeen fossil calibrations across primates and other mammalian groups and we select a subset of calibrations to date our mitogenomic tree. The divergence date estimates of the Strepsirrhine/Haplorhine split support an origin of crown primates in the Late Cretaceous, at around 74 Ma. This result supports a short-fuse model of primate origins, whereby relatively little time passed between the origin of the order and the diversification of its major clades. It also suggests that the early primate fossil record is likely poorly sampled.
Evaluating phylogenetic informativeness and data-type usage for new protein-coding genes across Vertebrata
2011, Molecular Phylogenetics and Evolution
Citation Excerpt :
For molecular studies, data from nuclear markers support the Theria hypothesis (Phillips and Penny, 2003; Hugall et al., 2007; Luo, 2007). Additional studies using DNA–DNA hybridization (Kirsch and Mayer 1988) and mitochondrial genomes (Janke et al., 2002; Zardoya et al., 2003) support the Marsupionta hypothesis, but these studies have been criticized due to their incomplete taxon sampling or bias due to base compositional heterogeneity (Grutzner and Graves, 2004). All three of the major mammal groups are represented by sequenced whole nuclear genomes, as we choose a subset to include in this study: Ornithorhynchus anatinus (monotreme), Monodelphis domestica (marsupial), and Mus musculus and Homo sapiens (placental).
As a resource for vertebrate phylogenetics, we developed 75 new protein-coding genes using a combination of expressed sequence tags (ESTs) available in Genbank, and targeted amplification of complementary DNA (cDNA). In addition, we performed three additional analyses in order to assess the utility of our approach. First, we profiled the phylogenetic informativeness of these new markers using the online program PhyDesign. Next, we compared the utility of four different data-types used in phylogenetics: nucleotides (NUCL), amino acids (AA), 1st and 2nd codon positions only (N12), and modified sequences to account for codon degeneracy (DEGEN1; Regier et al., 2010). Lastly, we use these new markers to construct a vertebrate phylogeny and address the uncertain relationship between higher-level mammal groups: monotremes, marsupials, and placentals. Our results show that phylogenetic informativeness of the 75 new markers varies, both in the amount of phylogenetic signal and optimal timescale. When comparing the four data-types, we find that the NUCL data-type, due to the high level of phylogenetic signal, performs the best across all divergence times. The remaining three data-types (AA, N12, DEGEN1) are less subject to homoplasy, but have greatly reduced levels of phylogenetic signal relative to NUCL. Our phylogenetic inference supports the Theria hypothesis of mammalian relationships, with marsupials and placentals being sister groups.
Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae)
2010, Molecular Phylogenetics and Evolution
The members of the cyprinid subfamily Danioninae form a diverse and scientifically important group of fishes, which includes the zebrafish, Danio rerio. The diversity of this assemblage has attracted much scientific interest but its monophyly and the relationships among its members are poorly understood. The phylogenetic relationships of the Danioninae are examined herein using sequence data from mitochondrial cytochrome b, mitochondrial cytochrome c oxidase I, nuclear opsin, and nuclear recombination activating gene 1. A combined data matrix of 4117 bp for 270 taxa was compiled and analyzed. The resulting topology supports some conclusions drawn by recent studies on the group and certain portions of the traditional classification, but our results also contradict key aspects of the traditional classification. The subfamily Danioninae is not monophyletic, with putative members scattered throughout Cyprinidae. Therefore, we restrict Danioninae to the monophyletic group that includes the following genera: Amblypharyngodon, Barilius, Cabdio, Chela, Chelaethiops, Danio, Danionella, Devario (including Inlecypris), Esomus, Horadandia, Laubuca, Leptocypris, Luciosoma, Malayochela, Microdevario, Microrasbora, Nematabramis, Neobola, Opsaridium, Opsarius, Paedocypris, Pectenocypris, Raiamas, Rasbora (including Boraras and Trigonostigma), Rasboroides, Salmostoma, Securicula, and Sundadanio. This Danioninae sensu stricto is divided into three major lineages, the tribes Chedrini, Danionini, and Rasborini, where Chedrini is sister to a Danionini–Rasborini clade. Each of these tribes is monophyletic, following the restriction of Danioninae. The tribe Chedrini includes a clade of exclusively African species and contains several genera of uncertain monophyly (Opsarius, Raiamas, Salmostoma). Within the tribe Rasborini, the species-rich genus Rasbora is rendered non-monophyletic by the placement of two monophyletic genera, Boraras and Trigonostigma, hence we synonymize those two genera with Rasbora. In the tribe Danionini, the miniature genus Danionella is recovered as the sister group of Danio, with D. nigrofasciatus sister to D. rerio.
The historical biogeography of the freshwater knifefishes using mitogenomic approaches: A Mesozoic origin of the Asian notopterids (Actinopterygii: Osteoglossomorpha)
2009, Molecular Phylogenetics and Evolution
The continental distributions of freshwater fishes in the family Notopteridae (Osteoglossomorpha) across Africa, India, and Southeast Asia constitute a long standing and enigmatic problem of freshwater biogeography. The migrational pathway of the Asian notopterids has been discussed in light of two competing schemes: the first posits recent transcontinental dispersal while the second relies on distributions being shaped by ancient vicariance associated with plate-tectonic events. In this study, we determined complete mitochondrial DNA sequences from 10 osteoglossomorph fishes to estimate phylogenetic relationships using partitioned Bayesian and maximum likelihood methods and divergence dates of the family Notopteridae with a partitioned Bayesian approach. We used six species representing the major lineages of the Notopteridae and seven species from the remaining osteoglossomorph families. Fourteen more-derived teleosts, nine basal actinopterygians, two coelacanths, and one shark were used as outgroups. Phylogenetic analyses indicated that the African and Asian notopterids formed a sister group to each other and that these notopterids were a sister to a clade comprising two African families (Mormyridae and Gymnarchidae). Estimated divergence time between the African and Asian notopterids dated back to the early Cretaceous when India–Madagascar separated from the African part of Gondwanaland. Thus, estimated time of divergence based on the molecular evidence is at odds with the recent dispersal model. It can be reconciled with the geological and paleontological evidence to support the vicariance model in which the Asian notopterids diverged from the African notopterids in Gondwanaland and migrated into Eurasia on the Indian subcontinent from the Cretaceous to the Tertiary. However, we could not exclude an alternative explanation that the African and Asian notopterids diverged in Pangea before its complete separation into Laurasia and Gondwanaland, to which these two lineages were later confined, respectively.
Cracking the nut: Geographical adjacency of sister taxa supports vicariance in a polytomic salamander clade in the absence of node support
2008, Molecular Phylogenetics and Evolution
Citation Excerpt :
Obtained sequences (lengths refer to the aligned sequences including gaps) comprised 540 bp in 16S and 465 bp in ATPase. Starting points are homologous to base pair positions 1937 (16S) and 7838 (ATPase) of the Lyciasalamandra atifi mitochondrial genome (formerly Mertensiella luschani atifi; GenBank Accession No. NC002756; Zardoya and Meyer, 2001; Zardoya et al., 2003). We almost consistently achieved ca. 1000 bp for all samples.
The urodelan genus Lyciasalamandra, which inhabits a relatively small area along the southern Turkish coast and some Aegean islands, provides an outstanding example of a diverse but phylogenetically unresolved taxon. Molecular trees contain a single basal polytomy that could be either soft or hard. We here use the information of nuclear (allozymes) and mitochondrial (fractions of the 16S rRNA and ATPase genes) datasets in combination with area relationships of lineages to resolve the phylogenetic relationships among Lyciasalamandra species in the absence of sufficient node support. We can show that neither random processes nor introgressive hybridization can be invoked to explain that the majority of pairs of sister taxa form geographically adjacent units and interpret that this pattern has been shaped by vicariant events. Topology discordance between mitochondrial and nuclear trees mainly refers to an affiliation of L. helverseni, a taxon restricted to the Karpathos archipelago, to the western-most and geographically proximate mainland taxon in the nuclear tree, while in the organelle tree it turns out to be the sister lineage to the geographically most distant eastern clade. As this discordance cannot be explained by long-branch attraction in either dataset we suppose that oversea dispersal may have accounted for a second colonization of the Karpathos archipelago. It may have initiated introgression and selection driven manifestation of alien eastern mitochondrial genomes on a western nuclear background. Our approach of testing for area relationships of sister taxa against the null hypothesis of random distribution of these taxa seems to be especially helpful in phylogenetic studies where traditional measures of phylogenetic branch support fail to reject the null hypothesis of a hard polytomy.
Ribosomal RNA genes and deuterostome phylogeny revisited: More cyclostomes, elasmobranchs, reptiles, and a brittle star
2007, Molecular Phylogenetics and Evolution
This is an expanded study of the relationships among the deuterostome animals based on combined, nearly complete 28S and 18S rRNA genes (>3925 nt.). It adds sequences from 20 more taxa to the ∼45 sequences used in past studies. Seven of the new taxa were sequenced here (brittle star Ophiomyxa, lizard Anolis, turtle Chrysemys, sixgill shark Hexanchus, electric ray Narcine, Southern Hemisphere lamprey Geotria, and Atlantic hagfish Myxine for 28S), and the other 13 were from GenBank and the literature (from a chicken, dog, rat, human, three lungfishes, and several ray-finned fishes, or Actinopterygii). As before, our alignments were based on secondary structure but did not account for base pairing in the stems of rRNA. The new findings, derived from likelihood-based tree-reconstruction methods and by testing hypotheses with parametric bootstrapping, include: (1) brittle star joins with sea star in the echinoderm clade, Asterozoa; (2) with two hagfishes and two lampreys now available, the cyclostome (jawless) fishes remain monophyletic; (3) Hexanchiform sharks are monophyletic, as Hexanchus groups with the frilled shark, Chlamydoselachus; (4) turtle is the sister taxon of all other amniotes; (5) bird is closer to the lizard than to the mammals; (6) the bichir Polypterus is in a monophyletic Actinopterygii; (7) Zebrafish Danio is the sister taxon of the other two teleosts we examined (trout and perch); (8) the South American and African lungfishes group together to the exclusion of the Australian lungfish. Other findings either upheld those of the previous rRNA-based studies (e.g., echinoderms and hemichordates group as Ambulacraria; orbitostylic sharks; batoids are not derived from any living lineage of sharks) or were obvious (monophyly of mammals, gnathostomes, vertebrates, echinoderms, etc.). Despite all these findings, the rRNA data still fail to resolve the relations among the major groups of deuterostomes (tunicates, Ambulacraria, cephalochordates and vertebrates) and of gnathostomes (chondrichthyans, lungfishes, coelacanth, actinopterygians, amphibians, and amniotes), partly because tunicates and lungfishes are rogue taxa that disrupt the tree. Nonetheless, parametric bootstrapping showed our RNA-gene data are only consistent with these dominant hypotheses: (1) deuterostomes consist of Ambulacraria plus Chordata, with Chordata consisting of tunicates and ‘vertebrates plus cephalochordates’; and (2) lungfishes are the closest living relatives of tetrapods.

View all citing articles on Scopus

View full text

Complete nucleotide sequence of the mitochondrial genome of a salamander, Mertensiella luschani

Abstract

Introduction

Section snippets

Mitochondrial DNA extraction

Organization of the salamander mitochondrial genome

Acknowledgments

J. Mol. Biol.

Gene

Mol. Phylogenet. Evol.

J. Biol. Chem.

Cell

Model of amino acid substitution in proteins encoded by mitochondrial DNA

J. Mol. Evol.

Mitochondrial DNA sequence divergence and phylogenetic relationships among eight chromosome races of the Sceloporus grammicus complex (Phrynosomatidae) in Central Mexico

Syst. Biol.

Comparison between the complete mtDNA sequences of the blue and the fin whale, two species that can hybridize in nature

J. Mol. Evol.

The complete mitochondrial DNA sequence of the shark Mustelus manazo: evaluating rooting contradictions to living bony vertebrates

Mol. Biol. Evol.

Vertebrate Paleontology and Evolution

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

Mol. Biol. Evol.

The complete nucleotide sequence, gene organization of carp (Cyprinus carpio) mitochondrial genome

J. Mol. Evol.

Interrelationships of basal sarcopterygians

The complete nucleotide sequence of the mitochondrial DNA of the dogfish, Scyliorhinus canicula

Genetics

A comprehensive set of sequence analysis programs for the VAX

Nucleic Acids Res.

Elongation of displacement loop strands in human and mouse mitochondrial DNA is arrested near specific template sequences

Proc. Natl. Acad. Sci. U. S. A.

Biology of Amphibians

Confidence limits on phylogenies: an approach using the bootstrap

Evolution

Amphibian Species of the World. A Taxonomic and Geographical Reference

The monotremes and the palimpsest theory

Bull. Am. Mus. Nat. Hist.

Analyses of mitochondrial DNA nest ratite birds within the Neoagnathae: supporting a neotenous origin of ratite morphological characters

Proc. R. Soc. Lond. B

The mtDNA sequence of the ostrich and the divergence between paleognathous and neognathous birds

Mol. Biol. Evol.

Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs

Proc. Natl. Acad. Sci. U. S. A.

MrBayes: bayesian inference of phylogeny

Bioinformatics

Complete mitochondrial DNA sequence of the Japanese sardine Sardinops melanostictus

Fish. Sci.

Complete mitochondrial DNA sequence of the Japanese eel, Anguilla japonica

Fish. Sci.

Complete mitochondrial DNA sequence of Conger myriaster (Teleostei: Anguilliformes): novel gene order for vertebrate mitochondrial genomes and the phylogenetic implications for anguilliform families

J. Mol. Evol.

The complete mitochondrial genome of Alligator mississipiensis and the separation between recent Archosauria (Birds and crocodiles)

Mol. Biol. Evol.

The marsupial mitochondrial genome and the evolution of placental mammals

Genetics

The mitochondrial genome of a monotreme-the platypus (Ornithorhynchus anatinus)

J. Mol. Evol.

The complete mitochondrial DNA sequence of Atlantic cod, Gadus morhua: relevance to taxonomic studies among cod-fishes

Mol. Mar. Biol.

The rapid generation of mutation data matrices from protein sequences

Comp. Appl. Biosci.

Complete mitochondrial DNA sequence of Aulopus japonicus (Teleostei: Aulopiformes), a basal Eurypterygii: longer DNA sequences and higher-level relationships

Ichthyol. Res.

Marsupials and Eutherians reunited: genetic evidence for the Theria hypothesis of mammalian evolution

Mammal. Genome