- Research article
- Open Access
Phylogenetic analyses of complete mitochondrial genome sequences suggest a basal divergence of the enigmatic rodent Anomalurus
© Horner et al; licensee BioMed Central Ltd. 2007
- Received: 25 September 2006
- Accepted: 08 February 2007
- Published: 08 February 2007
Phylogenetic relationships between Lagomorpha, Rodentia and Primates and their allies (Euarchontoglires) have long been debated. While it is now generally agreed that Rodentia constitutes a monophyletic sister-group of Lagomorpha and that this clade (Glires) is sister to Primates and Dermoptera, higher-level relationships within Rodentia remain contentious.
We have sequenced and performed extensive evolutionary analyses on the mitochondrial genome of the scaly-tailed flying squirrel Anomalurus sp., an enigmatic rodent whose phylogenetic affinities have been obscure and extensively debated. Our phylogenetic analyses of the coding regions of available complete mitochondrial genome sequences from Euarchontoglires suggest that Anomalurus is a sister taxon to the Hystricognathi, and that this clade represents the most basal divergence among sampled Rodentia. Bayesian dating methods incorporating a relaxed molecular clock provide divergence-time estimates which are consistently in agreement with the fossil record and which indicate a rapid radiation within Glires around 60 million years ago.
Taken together, the data presented provide a working hypothesis as to the phylogenetic placement of Anomalurus, underline the utility of mitochondrial sequences in the resolution of even relatively deep divergences and go some way to explaining the difficulty of conclusively resolving higher-level relationships within Glires with available data and methodologies.
- Compositional Homogeneity
- Compositional Bias
- Short Intersperse Nuclear Element
- Approximately Unbiased
- Complete Mitochondrial Genome Sequence
Phylogenetic relationships and divergence times within the superorder Glires (Rodentia, and Lagomorpha) remain controversial, with many discrepancies between estimates from morphological, molecular and fossil data. The problem is exacerbated both by the fact that Rodentia represents the most abundant and diversified order of living mammals and by variations in molecular evolutionary rate and mode in some families. For example, several molecular studies have suggested paraphyly of Rodentia or Glires [1–3], while others (and the majority of morphological data) support the monophyly of both groups [4–6]. Both molecular approaches and morphological analyses have their limitations. Critics of conclusions based on molecular characters cite the limited number of sequences considered and the apparent dependence of conclusions on the analytical methodologies employed, while adherents of molecular data point out that the predominantly dental and cranial characters employed in morphological analyses are likely subject to homoplastic evolution as a result of shared ecological constraints. Some intra-ordinal phylogenetic relationships in Rodentia also remain poorly resolved. For example, while the monophyly of many classically diagnosed Rodentia groups (Hystricognathi – a grouping of Myoxidae and Sciuridae – and the Muroidea/Dipodidae group) have been supported by molecular analyses (eg [4, 7]), relationships between these groups as well as the placement of a few under-studied taxa (such as the Anomaluridae) are controversial. Discrepancies between molecular and other data are not restricted to tree topologies. Molecular dating approaches (typically employing mitochondrial DNA sequences) have tended to provide estimates of divergence times which conflict with inferences drawn from the fossil record. More recently the availability of relaxed and local molecular clock approaches , which allow evolutionary rates to differ across the tree, has allowed some reconciliation of molecular and fossil derived divergence time estimates within Euarchontoglires [9, 10].
In the current study, we have sequenced and analysed the complete mitochondrial genome of Anomalurus sp. as a representative of the Anomaluridae, a family of flying squirrel-like rodents which possess two rows of pointed, raised scales on the undersides of their tails and whose cranial anatomy does not indicate a close relationship with sciurid flying squirrels. Indeed, the phylogenetic affinities of the Anomaluridae, which consists of three extant genera and whose geographic distribution is currently restricted to central Africa, have remained enigmatic owing both to the aforementioned weakness of morphological characters in the systematics of Rodentia and a relative lack of available molecular sequence data (currently restricted to five nuclear and two mitochondrial gene sequences). Previous studies based on molecular data have suggested alternative phylogenetic placements for Anomalurus, while weakly supporting various relationships between the Hystricognathi, the Sciuridae, and the Muroidea/Dipodidae group [11–13], while morphological classifications have suggested almost all possible placements for Anomalurus (reviewed in ).
We have performed extensive phylogenetic analyses of the protein coding regions of all available Primates, Lagomorpha and Rodentia mitochondrial genomes at both nucleotide and inferred amino acid sequence levels. We show that the sequence data suggest a phylogenetic affinity between Anomalurus and the Hystricognathi. However, statistical tests of alternative tree topologies do not exclude other phylogenetic hypotheses, either for the placement of Anomalurus sp. or for higher-level relationships within Rodentia. These observations are at least partially explained by a Bayesian relaxed molecular dating approach which generates estimates of divergence times within Euarchontoglires that are compatible with fossil and biogeographical data and suggest that a rapid evolutionary radiation within Glires occurred around 60 million years ago.
The mitochondrial genome of Anomalurus
The mtDNA of Anomalurus is 16,923 bp long and presents the common vertebrate gene organization. The entire genome sequence has been submitted to the EMBL sequence database under accession number AM_159537. Start and end positions of all protein coding, tRNA and rRNA genes were easily identifiable through homology searches using characterized mammalian mitochondrial protein sequences as probes. The control region (D-loop containing region) is 1439 bp long and shows the typical tripartite structure observed in mammals with the central conserved domain (15,770–16,062) and the CSB domain (16,063–16,923) both identifiable. Of the two conserved blocks known to be located in the ETAS domain, ETAS1 and ETAS2 , only a 40 bp long conserved sequence corresponding to ETAS1 can be identified (15641–15681). Indeed, only this element is conserved across Rodentia . The CSB domain includes all the three known conserved sequence blocks (CSB1, CSB2 and CSB3), and contains a tandem repeat array made up of a 40-fold repetition of an 8 bp long monomer (CGTACAGC).
While a concatenated dataset of unambiguously aligned regions of H-strand protein sequences (all protein-coding genes apart from NAD6) passed the compositional homogeneity test implemented in TREE-PUZZLE , many corresponding DNA sequences failed the equivalent test. Compositional heterogeneity was reduced by the removal of third codon positions from the DNA dataset, although several sequences still failed the chi square test. We have previously shown that first position synonymous leucine codon usage (Leu-SynP1) varies extensively between mitochondrial genomes and is a source of compositional heterogeneity . Accordingly, we removed (Leu-SynP1) codons from the alignment resulting in a dataset where only sequences from the Cercopithecinae (Papio, Macaca, Chlorocebus) failed the test of compositional homogeneity. Bearing this result in mind, phylogenetic analyses at the DNA level were performed both in the presence and absence of sequences from Primates.
Notably, and in accord with our previous analyses , monophyly of Rodentia is supported with high Bayesian posterior support for protein-based analyses. However, protein distance-based bootstrap support for this partition is low (30%). Inspection of bootstrap partitions reveals that decay in support of Rodentia monophyly is caused by the sequence of Anomalurus and to a lesser extent those of Thryonomys and Cavia (Hystricognathi) that have a tendency to cluster with the outgroup sequences. Likewise, the monophyly of Glires receives high posterior support but does not emerge on the bootstrap consensus tree, owing to a tendency of Lagomorpha to emerge basal to the Rodentia/(Primates + Dermoptera) divergence in some bootstrap datasets. In accordance with other molecular studies [11, 12], Bayesian analyses of protein sequences strongly support the monophyly of Hystricognathi, the monophyly of Myoxidae and Sciuridae and the monophyly of the Muroidea/Dipodidae grouping (all with BP = 100, PP = 1.0). In both Bayesian and distance bootstrap trees, Anomalurus emerges as sister of the Hystricognathi. Both methods suggest that the Hystricognathi/Anomalurus group is sister to a clade composed of Myoxidae/Sciuridae and the Muroidea/Dipodidae cluster. However, both the position of Anomalurus and the interrelationships between super-families within Rodentia receive only moderate posterior or bootstrap support. Bayesian analysis of the DNA data in the presence of the Cercopithecinae sequences yielded an identical tree topology apart from the position of Anomalurus which emerged as a poorly supported basal branch in the Primates/Dermoptera clade while Bayesian analyses of Glires, Scandentia and outgroup sequences alone generated an identical topology for Glires as the protein sequences (not shown).
Approximately Unbiased tests of selected alternative phylogenetic hypotheses of relationships within Euarchontoglires
1) Bayesian (protein) tree
2) Bayesian (DNA12) tree: (Glires,(Anomalurus/Primates/Dermoptera))
3) (Hystricognathi,((Dipodidae,Muroidea),(Anomalurus, (Sciurus,Glis))))
4) (Hystricognathi,((Sciurus,Glis),(Anomalurus, (Dipodidae,Muroidea))))
5) (Hystricognathi,(Sciurus,Glis)),(Anomalurus, (Dipodidae,Muroidea))))
6) Anomalurus basal in Rodentia
7) Anomalurus basal in Glires
8) ((Sciurus,Glis),((Hystricognathi,Anomalurus), (Dipodidae,Muroidea)))
9) ((Sciurus,Glis),(Hystricognathi,(Anomalurus, (Dipodidae,Muroidea))))
Distance bootstrap support (BS) for selected branches with indicated percentage of fastest evolving amino acid sites removed.
BS – 0%
BS – 5%
BS – 25%
Selected estimates of divergence dates and amino acid substitution rates in branches leading to the labelled divergence in Euarchontoglires.
aa substitution rate
4.11 – 7.76
4.39 – 8.76
7.00 – 11.44
7.73 – 12.74
13.13 – 17.75
13.23 – 17.90
31.86 – 42.12
32.58 – 42.81
44.34 – 54.77
46.83 – 59.14
56.72 – 65.96
54.90 – 65.62
61.05 – 67.53
61.04 – 67.27
62.32 – 70.99
61.87 – 70.97
basal Lagomorpha divergence
36.33 – 39.97
36.05 – 39.97
55.51 – 63.56
53.33 – 62.40
42.51 – 53.52
46.20 – 57.91
49.10 – 58.34
46.08 – 57.28
10.54 – 20.45
10.38 – 22.84
29.87 – 42.23
29.24 – 43.44
Variability and Numbers of constant sites for Euarchontoglires mitochondrial genes by taxonomic group
Protein vs. DNA sequences
The relative merits of performing phylogenetic analyses on nucleotide or corresponding amino acid sequences have been discussed extensively (eg ). In brief, while DNA sequences allow the complete parameterization of substitution models through the use of the data under examination, amino acid substitution models typically allow only amino acid frequencies to be adjusted according to the available data. On the other hand, the degree of substitutional saturation and homoplastic character evolution is expected to be higher among nucleotide sequences due to the restricted number of character states and mild to moderate compositional biases in DNA sequences are expected not to cause extensive perturbation of amino acid composition due to the degeneracy of the genetic code, but see . It is clearly desirable that DNA and associated inferred amino acid sequences should generate congruent phylogenetic hypotheses; in the absence of such congruent results it is necessary to assess whether inferences derived from DNA and protein sequences are statistically incongruent and, if so, attempt to explain observed differences in terms of characteristics of the data. In the current investigation, neither dataset discriminates between the two Bayesian consensus trees according to the approximately unbiased test. It is of some concern that the Bayesian consensus tree generated from the DNA data recovers Anomalurus not within Rodentia but among Primates. However, we note that the DNA dataset considered includes several primate sequences that fail the chi square test of compositional homogeneity. When Primates are excluded, Anomalurus is recovered in an identical position to the amino acid analyses (as sister to the Hystricognathi). Furthermore, while distance bootstrap analyses of protein sequences support, albeit weakly, the monophyly of Rodentia (Fig. 1), equivalent analyses performed on DNA sequences yield poorly supported consensus trees depicting non-monophyletic Glires, Rodentia and Primates/Dermoptera (not shown). Finally, no potential amino-acid synapomorphies link Anomalurus with the Primates/Dermoptera clade (while potential synapomorphies with the Hystricognathi and with the Muroidea/Dipodidae clade have been identified). We therefore consider results derived from protein sequences to be more reliable in this case, although we suggest that there is no significant incongruence between inferences derived from the protein and DNA data.
The phylogeny of Euarchontoglires and the evolutionary placement of Anomalurus
Bayesian and distance bootstrap analyses of concatenated first and second codon positions and inferred protein sequences of Rodentia, Primates/Dermoptera, Scandentia and Lagomorpha generated well-supported hypotheses of relationships within Primates/Dermoptera. In accordance with other analyses of mitochondrial sequences [21, 6], we recover Primates as paraphyletic with Dermoptera emerging as sister-group to the Anthropoidea with high bootstrap and posterior support. Our protein, but not DNA data reject monophyly of primates as assessed by the AU test of competing tree topologies. Analyses of concatenated nuclear (or nuclear and mitochondrial) data usually (eg [36–38]), but not always  prefer the traditional hypothesis of Primates monophyly. However, support for the position of Dermoptera as sister to Scandentia is often scarce and or dependent on the analytical method employed . The positioning of Tarsius as sister to Lemur and Nycticebus is unexpected in the light of morphological and nuclear data, but consistent with other analyses of mt (for discussion see ) and some analyses of nuclear data [39, 36]. The evolutionary affinities of Scandentia (represented in our analyses by Tupaia) have not been satisfactorily resolved by molecular data (see [40, 20, 39, 36, 37, 41, 21, 38] and references therein) although current thinking tends to favour a sister relationship with Dermoptera in a clade which emerges basal to the primates. The analyses of mt protein data presented here are in accord with our previous analyses of mt DNA data  in suggesting that Tupaia represents the basal divergence of Euarchontoglires rather than constituting the sister taxon of Lagomorpha, Primates, Primates/Dermoptera or Dermoptera. However, where tests of competing tree topologies have been performed, the position of Scandentia has remained unclear . Thus, while our mitochondrial dataset refutes what must be considered a weakly supported nuclear consensus for relationships between Dermoptera, Scandentia and Primates, it is not clear how inconsistent the nuclear data may be with the mitochondrially-derived hypothesis. Importantly, the question of Dermoptera/Primates relationships at least has recently been addressed through examination of the distribution of Short Interspersed Nuclear Elements in these organisms . These data should be free of many of the problems associated with analysis of molecular sequences (substitutional saturation, model choice, compositional bias etc) and strongly support the traditional hypothesis of Primate monophyly – suggesting that available mitochondrial and (to a lesser extent) nuclear sequence data have failed to correctly resolve Primates/Dermoptera relationships.
With respect to relationships within Glires, inferred protein sequences suggested a specific relationship between Anomalurus and the Hystricognathi. However, first and second codon positions of the gene sequences tended place Anomalurus among the basal divergences in the Primates/Dermoptera clade. This placement was not robustly supported and indeed Bayesian analyses of nucleotide sequences in the absence of Primates (some of whose sequences failed tests of compositional homogeneity) favoured the same placement as suggested by the protein sequences. While we are not aware of published hypotheses suggesting this relationship, it should be noted that a relationship between Anomaluridae and Ctenodactylidae has been proposed on the basis of morphological features . Recent molecular and many classical studies have suggested an affinity between Hystricognathi and Ctenodactylidae (e.g. [11, 7, 13]). Unfortunately, at the present time, no complete mitochondrial genome sequences from Ctenodactylidae are available. Some molecular data have suggested that the Anomaluridae are specifically related to the Pedetidae (Spring Hares) . Recent analyses that have included sequences from either of these taxa have tended to place these organisms as weakly supported basal branches in a clade containing Dipodidae, Muridae, Geomyidae and Heteromyidae (sister to the Dipodidae/Muroidea clade in our sampling) [36, 11, 7, 43]. Our analyses of constrained tree topologies recovered this placement as a viable alternative to our preferred hypothesis of a relationship between Anomalurus and Hystricognathi (and presumably Ctenodactylidae).
With respect to relationships between other families/superfamilies within Rodentia, we consistently recover previously proposed relationships between Dipodidae and Muroidea and between Sciuroidea and Gliridae with high bootstrap and posterior probability support. Our analyses however, like those based on other genes or gene concatenations [39, 36, 37, 41, 11, 12, 38, 7, 43] fail to unambiguously resolve relationships between these groups and the Hystricognathi in the sense that high posterior probabilities for higher order relationships within Rodentia are often accompanied by moderate or low bootstrap support and valid probabilistic tests of alternative topologies have seldom been presented. While our data and analyses prefer the hypothesis that the basal divergence within Rodentia consists of Hystricognathi (and by inference Ctenodactylidae) + Anomaluridae, leaving the Dipodidae/Muroidea and Gliridae/Sciuridae clades as sisters to each other, our data do not exclude a multitude of other evolutionary scenarios.
The Slow-Fast method – in which faster evolving sites are progressively removed from the dataset and changes in support for nodes of interest are examined – was employed to investigate whether sites supporting different hypotheses of relationships could be partitioned according to evolutionary rates. Exclusion of fast evolving sites has little impact on the resolution of either the position of Anomalurus (when the 25% of sites inferred to be fastest evolving were removed, we recover Anomalurus as a weakly supported sister to the Muridae/Dipodidae clade in accordance with constrained topologies discussed previously) or other relationships within Rodentia, suggesting that "noise" from fast evolving sites is not obscuring phylogenetic signal present in slower evolving sites. We interpret this finding as an indication that phylogenetic signal for higher-order relationships within Rodentia is rather scarce. In accordance with this proposal, we observe that the inferred amino acid sequences derived from Anomalurus (3519 unambiguously aligned amino acids) share only three potential synapomorphies with the Hystricognathi and three with the Muroidea/Dipodidae clade. There are no potential synapomorphies linking all Rodentia, or associating Anomalurus with Lagomorpha, the Myoxidae/Sciuridae clade, Primates/Dermoptera, or any possible sister group set of Rodentia families.
Molecular dating of divergences in Euarchontoglires
Molecular dating of divergences within Euarchontoglires based on mitochondrial sequence data and a global molecular clock has historically yielded estimates in conflict with the fossil record, particularly with respect to Rodentia e.g. [44, 45]. More recently several approaches that allow substitution rates to vary over the tree have been developed (for review see ). We have employed a Bayesian relaxed molecular clock approach that does not require the user to specify where rate changes occur on the tree and allows specification of calibration points as intervals rather than fixed dates. Using 6 constraints (upper and lower limits on three nodes) we have generated estimates of divergence times which are highly consistent with estimates of divergence dates based on the fossil record. Notably, the divergence dates recovered for Homo vs. Pan (5.7 and 6.4MYA for Protein and DNA data respectively), old world vs. new world monkeys (36.8 and 38.5MYA for Protein and DNA data) are highly consistent with both fossil data and other recent molecular dating studies using molecular sequences . We estimate that the divergence of Rodentia occurred 62.8 (protein) or 62.7 (DNA) MYA, the divergence of Hystricognathi + Anomalurus occurred 58.8 (protein) or 57.5 (DNA) MYA while the divergence of Anomalurus occurred 48.1 (protein) or 52.3 (DNA) MYA and the divergence of the Sciuidae/Myoxidae and Muroidea/Dipodidae clades occurred 53.6 (protein) or 51.8 (DNA) MYA – with the Mus/Rattus split occurring 15.1 (protein) or 15.9 (DNA) MYA. These estimates are generally consistent with the fossil data and recent estimates using local clock approaches [13, 9, 10].
Given the relative lack of resolution of relationships within Rodentia, we were interested to investigate the impact of the tree topology on estimates of divergence dates. Changes in the phylogenetic position of Anomalurus yielded relatively minor differences in divergence time estimates. For example, placing Anomalurus as the basal divergence in Rodentia or as sister to the Dipodidae/Muroidea/Myoxidae/Sciuridae group altered estimates of divergence of Rodentia and Lagomorpha by a maximum of 0.12MY. Estimates of the divergence of the Hystricognathi lineage from the Dipodidae/Muroidea/Myoxidae/Sciuridae never varied by more than 3.5MY and the divergence of Anomalurus by at most 2.8MY (not shown).
These findings are notable as they highlight a fundamental problem in the resolution of higher order relationships within Rodentia. Accounting for the 5% error intervals of our dating estimates, the divergence of Rodentia from Lagomorpha, the divergence of Hystricognathi from other Rodentia and the divergence of Sciuridae/Myoxidae and Muroidea/Dipodidae potentially occurred within 3.1 million years of each other around 60 million years ago – leaving relatively little time for the evolution of lineage-specific characters (molecular or morphological) which may be used in the reconstruction of phylogenetic affinities. Conversely, the relatively long subsequent independent evolutionary history of lineages considered here, in conjunction with the limited available taxonomic sampling is likely to have lead to extensive symplesiomorphy and homoplasy, further complicating phylogenetic reconstruction.
The use of mitochondrial sequences for the investigation of even relatively shallow phylogenetic relationships within Rodentia has recently been questioned [47, 48]. Indeed it has long been suspected that fast evolutionary rates and compositional biases can lead to misleading phylogenetic signal and poorly supported splits for deeper relationships. While we agree that saturation and compositional biases present a major problem for the reconstruction of ancient divergences, we stress that conclusions from mitochondrial sequences regarding divergence times are consistent with fossil data. Indeed recent studies using individual and concatenated nuclear or nuclear and mitochondrial gene sequences also fail to robustly resolve higher-level relationships within Rodentia [36, 37, 11, 12, 38]. Given the aforementioned considerations, we suggest that difficulties in the reconstruction of correct and unambiguous higher-order relationships within Glires do not reflect limitations of either nuclear or mitochondrial sequence data, but are likely to be inherent consequences of a rapid evolutionary radiation which occurred around 60 million years ago.
DNA extraction, amplification and sequencing
Mitochondrial DNA was extracted from 4.5 g of frozen liver of an Anomalurus sp (scaly-tailed flying squirrel) specimen captured in central Africa (specimen provided by F. Catzeflis), according to previously described methods for mammalian species .
The entire mitochondrial genome was amplified, using the Polymerase Chain Reaction with eight pairs of heterologous primers designed on the basis of highly conserved regions of the complete mitochondrial sequence of several representative species mammalian species . Amplifications were performed in 100 μl reaction volumes containing 10 mM Tris-HCl (pH 8.3), 50 mM KCl, 1.5 mM MgCl2, 0.001% (w/v) gelatin, 0.25 mM of each dNTP, 0.5 μM of each primer, and 2.5U of TaqGold polymerase (Roche Applied Science). PCR cycling conditions were 10 min of hot start at 95°C for the activation of the enzyme, followed by 30–35 amplification cycles (45 s of denaturation at 95°C, 45 s of primer annealing at temperatures from 55 to 65°C, and 2 to 3 min of extension at 72°C) followed by a final cycle of 7 min at 72°C. Single amplification products with length between 1.2 and 3.5 Kb were consistently obtained and produced overlapping fragments that covered the whole mitochondrial genome. PCR products were purified using the Amicon Microcon-PCR Centrifugal Filter Devises (Millipore) following the manufacturer's instructions. Fragments were sequenced either directly or after cloning in the pGEM-t easy vector (Promega). Sequencing reactions were performed using the Thermo Sequenase Cy5.5 Dye Terminator Cycle Sequencing Kit (Amersham Pharmacia Biotech) in 8 μl reaction volumes and following the manufacturer's instructions. After purification, DNA sequences were analyzed on a Seq4×4 automated sequencer (Amersham Pharmacia Biotech). Double strand primer walking strategy provided contiguous sequence information for both strands in all fragments. All overlapping regions between amplified fragments matched perfectly and all predicted open reading frames followed the vertebrate mitochondrial genetic code, leading us to exclude the possibility that we had amplified fragments of mitochondrial genome that had been inserted into the nuclear genome. The mtDNA sequence of the flying squirrel Anomalurus sp. has a G+C content of 46.16% and has been deposited in the EMBL database under the accession number AM_159537.
Conceptually translated coding sequences H-strand genes derived from all available complete mitochondrial genomes of Primates, Dermoptera, Scandentia, Rodentia and Lagomorpha species were aligned using the program MUSCLE  [see Additional file 1]. Sequences from the Laurasiatheria species sheep, dog and mole were included as outgroups (a total of 41 taxa, see table included in supplementary materials). Alignments were manually adjusted and DNA sequences reverse aligned to correspond with protein alignments. Regions of low alignment quality were identified using the program G-Blocks  and excluded from subsequent analyses. Protein sequences and the ungapped first and second codon positions (after exclusion of codons with first position leucine synonymous substitutions (Leu-SynP1)) of DNA sequences, were included in concatenated datasets for phylogenetic analyses (5358 nucleotides, 3519 amino acids).
Phylogenetic analyses were carried out using the program MrBayes 3.1  using the General-Time-Reversible (GTR) substitution model for nucleotide sequences and "mtrev24" model for protein sequences, in both cases with the invariant site plus gamma options (eight categories). Two parallel analyses, each composed of one cold and three incrementally heated chains were run for 2,000,000 generations. Trees were sampled every 50 generations and 20,000 trees were discarded as "burn-in" (sufficient to allow convergence according to the tests indicated by the program).
Distance bootstrap analyses were performed by using the shellscript PUZZLEBOOT (available from the TREE_PUZZLE website) in conjunction with TREE-PUZZLE  and the programs SEQBOOT, NEIGHBOR and CONSENSE from the PHYLIP package , using the substitution models employed in Bayesian analyses with rate heterogeneity parameters estimated by TREE-PUZZLE on the relevant Bayesian tree topology.
For tests of alternative tree topologies, site likelihoods were calculated under the GTR + gamma and mtrev24 + gamma models (for DNA and protein data respectively) using the PAML package . The Approximately Unbiased (AU) tests were performed using the software CONSEL .
Bayesian relaxed molecular clock dating analyses were performed using the MULTIDISTRIBUTE package  in conjunction with programs from the package PAML. For DNA sequences, the F85 + gamma model (the most complex model available in BASEML) was employed. For protein sequences, following the method of Amer and Kumazawa , a modified version of CODEML was used to estimate model parameters for the mtrev24 + gamma model. In both cases the program ESTBRANCHES  was used to estimate variances of branch lengths and MULTIDIVTIME  used to estimate divergence times.
Analyses of compositional homogeneity were performed using the Chi square test implemented in the program TREE-PUZZLE. Site-specific relative substitution rates were estimated using the SiteVarProt algorithm .
The authors would like to thank F. Catzeflis for providing the Anomalurus sp. specimen from which mitochondrial DNA was isolated. Work presented in this manuscript was partially funded by grants from the Ministero dell'Istruzione, Universita' e Ricerca, Italy (FIRB and FIRST).
- Graur D, Duret L, Gouy M: Phylogenetic position of the order Lagomorpha (rabbits, hares and allies). Nature. 1996, 379: 333-335. 10.1038/379333a0.View ArticlePubMedGoogle Scholar
- Graur D, Hide WA, Li WH: Is the guinea-pig a rodent?. Nature. 1991, 351: 649-652. 10.1038/351649a0.View ArticlePubMedGoogle Scholar
- D'Erchia AM, Gissi C, Pesole G, Saccone C, Arnason U: The guinea-pig is not a rodent. Nature. 1996, 381: 597-600. 10.1038/381597a0.View ArticlePubMedGoogle Scholar
- Douzery EJP, Huchon D: Rabbits, if anything, are likely Glires. Mol Phylogenet Evol. 2004, 33: 922-935. 10.1016/j.ympev.2004.07.014.View ArticlePubMedGoogle Scholar
- Reyes A, Gissi C, Catzeflis F, Nevo E, Pesole G, Saccone C: Congruent mammalian trees from mitochondrial and nuclear genes using Bayesian methods. Mol Biol: Evol. 2004, 21: 397-403. 10.1093/molbev/msh033.View ArticleGoogle Scholar
- Lin YH, Waddell P, Penny D: Pika and vole mitochondrial genomes increase support for both rodent monophyly and Glires. Gene. 2002, 294: 119-129. 10.1016/S0378-1119(02)00695-9.View ArticlePubMedGoogle Scholar
- Adkins RM, Walton AH, Honeycutt RL: Higher-level systematics of rodents and divergence time estimates based on two congruent nuclear genes. Mol Phylogenet Evol. 2003, 26: 409-420. 10.1016/S1055-7903(02)00304-4.View ArticlePubMedGoogle Scholar
- Welch JJ, Bromham L: Molecular dating when rates vary. Trends Ecol Evol. 2005, 20: 320-327. 10.1016/j.tree.2005.02.007.View ArticlePubMedGoogle Scholar
- Hasegawa M, Thorne J, Kishino H: Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution. Genes Genet Syst. 2003, 78: 267-283. 10.1266/ggs.78.267.View ArticlePubMedGoogle Scholar
- Springer MS, Murphy WJ, Eizerik E, O'Brien SJ: Placental mammal diversification and the Cretaceous–Tertiary boundary. Proc Natl Acad Sci USA. 2003, 100: 1056-1061. 10.1073/pnas.0334222100.PubMed CentralView ArticlePubMedGoogle Scholar
- Douzery EJP, Delsuc F, Stanhope MJ, Huchon D: Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations. J Mol Evol. 2003, 57: S201-S203. 10.1007/s00239-003-0028-x.View ArticlePubMedGoogle Scholar
- Huchon D, Madsen O, Sibbald MJJB, Ament K, Stanhope MJ, Catzeflis F, de Jong WW, Douzery EJP: Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes. Mol Biol: Evol. 2002, 19: 1053-1065.View ArticleGoogle Scholar
- Montgelard C, Bentz S, Tirard C, Verneau O, Catzeflis F: Molecular systematics of Sciurognathi (Rodentia): The mitochondrial cytochrome b and 12s rrna genes support the Anomaluroidea (Petidae and Anomaluridae). Mol Phylogenet Evol. 2002, 22: 220-233. 10.1006/mpev.2001.1056.View ArticlePubMedGoogle Scholar
- Luckett WP, Hartenberger JL: Evolutionary relationships among rodents - Comments and conclusions. Evolutionary Relationships Among Rodents. Edited by: Luckett WP and Hartenberger JL. 1985, New York, PlenumView ArticleGoogle Scholar
- Sbisa E, Tanzariello F, Reyes A, Pesole G, Saccone C: Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications. Gene. 1997, 205: 125-140. 10.1016/S0378-1119(97)00404-6.View ArticlePubMedGoogle Scholar
- Larizza A, Pesole G, Reyes A, Sbisa E, Saccone C: Lineage specificity of the evolutionary dynamics of the mtDNA D-loop region in rodents. J Mol Evol. 2002, 54: 145-155. 10.1007/s00239-001-0063-4.View ArticlePubMedGoogle Scholar
- Schmidt HA, Strimmer K, Vingron M, von Haesler A: TREE_PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 2002, 18: 502-504. 10.1093/bioinformatics/18.3.502.View ArticlePubMedGoogle Scholar
- Schmitz J, Ohme M, Zischler H: The complete mitochondrial sequence of Tarsius bancanus: evidence for an extensive nucleotide compositional plasticity of primate mitochondrial DNA. Mol Biol: Evol. 2002, 19: 544-553.View ArticleGoogle Scholar
- Shimodaira H: An approximately unbiased test of phylogenetic tree selection. Syst Biol. 2002, 51: 492-508. 10.1080/10635150290069913.View ArticlePubMedGoogle Scholar
- Schmitz J, Ohme M, Zischler H: The complete mitochondrial genome of Tupaia belangeri and the phylogenetic affiliation of Scandentia to other eutherian orders. Mol Biol: Evol. 2000, 17: 1334-1343.View ArticleGoogle Scholar
- Arnason U, Adegoke JA, Bodin K, Born EW, Esa YB, Gullberg A, Nilsson M, Short RV, Xu X, Janke A: Mammalian mitogenomic relationships and the root of the eutherian tree. Proc Natl Acad Sci USA. 2002, 99: 8151-10.1073/pnas.102164299.PubMed CentralView ArticlePubMedGoogle Scholar
- Brinkmann H, Philippe H: Archae a sister group of Bacteria? Indications from tree reconstruct on artifacts in ancient phylogenies. Mol Biol: Evol. 1999, 16: 817-825.View ArticleGoogle Scholar
- Horner DS, Pesole G: The estimation of relative site variability among aligned homologous protein sequences. Bioinformatics. 2003, 19: 600-606. 10.1093/bioinformatics/btg063.View ArticlePubMedGoogle Scholar
- Thorne J, Kishino H: Divergence time and evolutionary rate estimation with multilocus data. Syst Biol. 2002, 51: 689-702. 10.1080/10635150290102456.View ArticlePubMedGoogle Scholar
- Amer SAM: Mitochondrial genome of Pogona vitticepes (Reptilia; Agamidae): control region duplication and the origin of Australasian agamids. Gene. 2005, 346: 249-256. 10.1016/j.gene.2004.11.014.View ArticlePubMedGoogle Scholar
- Meng J, Wyss AR, Dawson MR, Zhai R: Primitive fossil rodent from Inner Mongolia and its implications for mammalian phylogeny. Nature. 1994, 370: 134-136. 10.1038/370134a0.View ArticlePubMedGoogle Scholar
- Archibald DJ, Averianov AO, Ekdale EG: Late Cretaceous relatives of rabbits, rodents, and other extant eutherian mammals. Nature. 2001, 414: 62-65. 10.1038/35102048.View ArticlePubMedGoogle Scholar
- McKenna MC, Bell SK: Classification of mammals above the species level. 1997, New York, Columbia University PressGoogle Scholar
- Waddell P, Penny D: Evolutionary trees of apes and humans from DNA sequences. Handbook of Human Symbolic Evolution. Edited by: Lock AJ and Peters CR. 1996, Oxford, Oxford University Press, 53-73.Google Scholar
- Kumar S, Filipski A, Swarna V, Walker A, Hedges SB: Placing confidence limits on the molecular age of the human–chimpanzee divergence. Proc Natl Acad Sci USA. 2005, 102: 18842-18847. 10.1073/pnas.0509585102.PubMed CentralView ArticlePubMedGoogle Scholar
- Lomax MI, Hewett-Emmett D, Yang TL, Grossman LI: Rapid evolution of the human gene for cytochrome c oxidase subunit IV. Proc Natl Acad Sci USA. 1992, 89: 5266-5270. 10.1073/pnas.89.12.5266.PubMed CentralView ArticlePubMedGoogle Scholar
- Andrews DT, Easteal S: Evolutionary rate acceleration of cytochrome c oxidase subunit I in simian primates. J Mol Evol. 2000, 47: 562-568.Google Scholar
- Andrews DT, Jermiin LS, Easteal S: Accelerated evolution of cytochrome b in simian primates: adaptive evolution in concert with other mitochondrial proteins?. J Mol Evol. 1998, 47: 249-257. 10.1007/PL00006382.View ArticlePubMedGoogle Scholar
- Delsuc F, Phillips MJ, Penny D: Comment on "Hexapod origins, monophyletic or paraphyletic". Science. 2003, 301: 1482d-1483d. 10.1126/science.1086558.View ArticleGoogle Scholar
- Foster PG, Jermiin LS, Hickey DA: Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria. J Mol Evol. 1997, 44: 282-288. 10.1007/PL00006145.View ArticlePubMedGoogle Scholar
- Murphy WJ, Eizerik E, Johnson WE, Zhang TP, Ryder OA, O'Brien SJ: Molecular phylogenetics and the origins of placental mammals. Nature. 2001, 409: 614-618. 10.1038/35054550.View ArticlePubMedGoogle Scholar
- Murphy WJ, Eizerik E, O'Brien SJ, Madsen O, Scally M, Douady C, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS: Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 2001, 294: 2347-2351. 10.1126/science.1067179.View ArticleGoogle Scholar
- Waddell P, Shelley S: Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, c-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models. Mol Phylogenet Evol. 2002, 28: 197-224. 10.1016/S1055-7903(03)00115-5.View ArticleGoogle Scholar
- Eizerik E, Murphy WJ, O'Brien SJ: Molecular dating and biogeography of the early placental mammal radiation. J Hered. 2001, 92: 212-219. 10.1093/jhered/92.2.212.View ArticleGoogle Scholar
- Adkins RM, Honeycutt RL: Molecular phylogeny of the superorder Archonta. Proc Natl Acad Sci USA. 1991, 88: 10317-10321. 10.1073/pnas.88.22.10317.PubMed CentralView ArticlePubMedGoogle Scholar
- Amrine-Madsen H, Koepfli KP, Waynes RK, Springer MS: A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships. Mol Phylogenet Evol. 2002, 28: 225-240. 10.1016/S1055-7903(03)00118-0.View ArticleGoogle Scholar
- Schmitz J, Ohme M, Suryobrotu B, Zischler H: The Colugo (Cynocephalus variegatus, Dermoptera): The primates’ gliding sister?. Mol Biol: Evol. 2002, 19: 2308-2312.View ArticleGoogle Scholar
- DeBry RW: Identifying conflicting signal in a multigene analysis reveals a highly resolved tree: the phylogeny of Rodentia (Mammalia). Syst Biol. 2003, 52: 604-617. 10.1080/10635150390235403.View ArticlePubMedGoogle Scholar
- Kumar S, Hedges SB: A molecular timescale for vertebrate evolution. Nature. 1998, 392: 917-920. 10.1038/31927.View ArticlePubMedGoogle Scholar
- Janke A, Xu X, Arnason U: The complete mitochondrial genome of the walllaroo (Macropus robustus) and the phylogenetic relations among the monotremata. Proc Natl Acad Sci USA. 1997, 94: 1276-1281. 10.1073/pnas.94.4.1276.PubMed CentralView ArticlePubMedGoogle Scholar
- Raaum RL, Sterner KN, Noviello CM, Stewart CB, Disotell TR: Catarrhine primate divergence dates estimated from complete mitochondrial genomes: concordance with fossil and nuclear DNA evidence. J Human Evol. 2005, 48: 237-257. 10.1016/j.jhevol.2004.11.007.View ArticleGoogle Scholar
- Steppan SJ, Adkins RM, Spinks PQ, Hale C: Multigene phylogeny of the Old World mice, Murinae, reveals distinct geographic lineages and the declining utility of mitochondrial genes compared to nuclear genes. Mol Phylogenet Evol. 2005, 37: 370-388. 10.1016/j.ympev.2005.04.016.View ArticlePubMedGoogle Scholar
- Springer MS, DeBry RW, Douady C, Amrine HM, Madsen O, de Jong WW, Stanhope MJ: Mitochondrial versus nuclear gene sequences in deep-level mammalian phylogeny reconstruction. Mol Biol: Evol. 2003, 18: 132-143.View ArticleGoogle Scholar
- Arnason U, Gullberg A, Widegren B: The complete nucleotide sequence of the mitochondrial DNA of the fin whale, Balaenoptera physalus. J Mol Evol. 1991, 33: 556-568. 10.1007/BF02102808.View ArticlePubMedGoogle Scholar
- Edgar RC: MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004, 5:Google Scholar
- Castresana J: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol: Evol. 2000, 17: 540-552.View ArticleGoogle Scholar
- Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003, 19: 1572-1574. 10.1093/bioinformatics/btg180.View ArticlePubMedGoogle Scholar
- Felsenstein J: PHYLIP - Phylogeny Inference Package (version 3.2). Cladistics. 1989, 5: 164-166.Google Scholar
- Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS. 1994, 13: 555-556.Google Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.