Mitochondrial phylogeny of hedgehogs and monophyly of Eulipotyphla

Sequencing and analysis of the complete mitochondrial genome of the lesser bandicoot rat (Bandicota bengalensis) from China and its phylogenetic analysis

The complete mitogenome sequence of the lesser bandicoot rat (Bandicota bengalensis Gray and Hardwicke, 1833) was determined using long PCR. The genome was 16,327 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 origin of L strand replication and 1 control region. The overall base composition of the heavy strand is A (34.2%), C (24.9%), T (28.5%) and G (12.4%). The base compositions present clearly the A-T skew, which is most obviously in the control region and protein-coding genes. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees. This study verifies the evolutionary status of Bandicota bengalensis in Muridae at the molecular level. The mitochondrial genome would be a significant supplement for the Bandicota bengalensis genetic background. The two Bandicota species formed a monophyletic group with the high bootstrap value (100%) in all examinations.

Sequencing and analysis of the complete mitochondrial genome of Ochotona hyperborea from China and its phylogenetic analysis

The complete mitogenome sequence of Ochotona hyperborea was determined using long PCR. The genome was 17,063 bp in length and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one origin of L strand replication, and one control region. The overall base composition of the heavy strand is A (31.1%), C (28.7%), T (26.3%), and G (13.9%). The base compositions present clearly the A-T skew, which is most obvious in the control region and protein-coding genes. Mitochondrial genome analyses based on MP, ML, NJ, and Bayesian analyses yielded identical phylogenetic trees. This study verifies the evolutionary status of Ochotona hyperborea in Ochotonidae at the molecular level. The mitochondrial genome would be a significant supplement for the Ochotona hyperborea genetic background. The eight Ochotona species formed a monophyletic group with the high bootstrap value (100%) in all examinations.

Sequencing and analysis of the complete mitochondrial genome of Micromys erythrotis from China and its phylogenetic analysis

The complete mitogenome sequence of Micromys erythrotis was determined using long PCR. The genome was 16,238 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 origin of L strand replication and 1 control region. The overall base composition of the heavy strand is A (33.7%), C (24.8%), T (29.1%) and G (12.4%). The base compositions present clearly the A-T skew, which is most obviously in the control region and protein-coding genes. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees. This study verifies the evolutionary status of Micromys erythrotis in Muridae at the molecular level. The mitochondrial genome would be a significant supplement for the Micromys erythrotis genetic background.

Sequencing and analysis of the complete mitochondrial genome of Blarinella griselda from China and its phylogenetic analysis

The complete mitogenome sequence of Blarinella griselda was determined using long PCR. The genome was 16,947 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 origin of L strand replication and 1 control region. The overall base composition of the heavy strand is A (33.1%), C (22.6%), T (31.6%) and G (12.7%). The base compositions present clearly the A-T skew, which is most obviously in the control region and protein-coding genes. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees. This study verifies the evolutionary status of Blarinella griselda in Soricidae at the molecular level. The mitochondrial genome would be a significant supplement for the Blarinella griselda genetic background. The three Blarinella species formed a monophyletic group with the high bootstrap value (100%) in all examinations.

Sequencing and analysis of the complete mitochondrial genome of Crocidura tanakae from China and its phylogenetic analysis

The complete mitogenome sequence of Crocidura tanakae was determined using long PCR. The genome was 16,969 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 origin of L strand replication and 1 control region. The overall base composition of the heavy strand is A (32.5%), C (22.3%), T (31.9%), and G (13.3%). The base compositions present clearly the A-T skew, which is most obviously in the control region and protein-coding genes. Mitochondrial genome analyses based on MP, ML, NJ, and Bayesian analyses yielded identical phylogenetic trees. The five Crocidura species formed a monophyletic group with the high bootstrap value (100%) in all examinations. This study verifies the evolutionary status of C. tanakae in Soricidae at the molecular level. The mitochondrial genome would be a significant supplement for the C. tanakae genetic background.

Sequencing and analysis of the complete mitochondrial genome of Chodsigoa hoffmanni from China and its phylogenetic analysis

The complete mitogenome sequence of Chodsigoa hoffmanni was determined using long PCR. The genome was 17,138 bp in length and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one origin of L strand replication, and one control region. The overall base composition of the heavy strand is A (32.8%), C (24.4%), T (29.8%), and G (13.0%). The base compositions present clearly the A-T skew, which is most obviously in the control region and protein-coding genes. Mitochondrial genome analyses based on MP, ML, NJ, and Bayesian analyses yielded identical phylogenetic trees. Chodsigoa hoffmanni is the first species to have been reported on the mitochondrial genome in Chodsigoa genus. This study verifies the evolutionary status of C. hoffmanni in Soricidae at the molecular level. The mitochondrial genome would be a significant supplement for the C. hoffmanni genetic background.

Information Criteria for Comparing Partition Schemes

When inferring phylogenies, one important decision is whether and how nucleotide substitution parameters should be shared across different subsets or partitions of the data. One sort of partitioning error occurs when heterogeneous subsets are mistakenly lumped together and treated as if they share parameter values. The opposite kind of error is mistakenly treating homogeneous subsets as if they result from distinct sets of parameters. Lumping and splitting errors are not equally bad. Lumping errors can yield parameter estimates that do not accurately reflect any of the subsets that were combined whereas splitting errors yield estimates that did not benefit from sharing information across partitions. Phylogenetic partitioning decisions are often made by applying information criteria such as the Akaike information criterion (AIC). As with other information criteria, the AIC evaluates a model or partition scheme by combining the maximum log-likelihood value with a penalty that depends on the number of parameters being estimated. For the purpose of selecting an optimal partitioning scheme, we derive an adjustment to the AIC that we refer to as the AIC$^{(p)}$ and that is motivated by the idea that splitting errors are less serious than lumping errors. We also introduce a similar adjustment to the Bayesian information criterion (BIC) that we refer to as the BIC$^{(p)}$. Via simulation and empirical data analysis, we contrast AIC and BIC behavior to our suggested adjustments. We discuss these results and also emphasize why we expect the probability of lumping errors with the AIC$^{(p)}$ and the BIC$^{(p)}$ to be relatively robust to model parameterization.

Complete mitochondrial genome of the Iberian Mole Talpa occidentalis (Talpidae, Insectivora) and comparison with Talpa europaea

The complete mitogenome of Talpa occidentalis, the Iberian mole, was sequenced using a combination of the Illumina and Sanger methods. The 16,962 bp genome obtained contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a control region. Thirty-seven identical repetitions of a 10-nucleotide (CACACGTACG) repeat element were identified in the non-coding control region (D-loop). The number, order, and orientation of the mitochondrial genes are the same as in T. europaea, the only mitogenome published so far for this genus. These two mitogenomes differ only at the repeat element included in the control region. The phylogeny obtained for the Talpidae species using the protein-coding genes of these mitogenomes agrees with the current classification of this family.

Regional Diversity and Diversification in Mammals

The effects of regional diversity on diversification remain controversial. The classic hypothesis that diversification decelerates as regional diversity increases has been recently revived. Yet, there is little geographic evidence for slower diversification across regions of high diversity, and diversity is often thought to promote diversification through its effects on ecological divergence and speciation. Here, we use the newest phylogeny for mammals (4,990 species) and two different methods to test the effects of regional diversity on diversification. We find that regions of high diversity are dominated by expanding clades that are far from their estimated carrying capacities. Regions of low diversity host clades that are small and mostly saturated. These results were supported across mammals and their six largest orders. They were corroborated by the two methods when controlling for clade relatedness, clade nestedness, and clade size. Together, these results reject the hypothesis that high geographic concentration of mammals effectively suppresses their further diversification. Instead, highly diverse regions (especially the tropics) seem to act as the engine of mammalian richness.

The complete mitochondrial genome of the small-toothed forest hedgehog Mesechinus miodon (Eulipotyphla: Erinaceidae)

The complete mitochondrial genome of the small-toothed forest hedgehog Mesechinus miodon (Eulipotyphla: Erinaceidae) has been reconstructed from Illumina sequencing data. The circular genome is 16 842 bp long, comprising 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), and one control region. All PCGs are initiated with ATR (ATA/ATG) codons, except for nad4 with GTG as its initiation codon. Two PCGs (cox3 and nad4) harbor an incomplete termination codon T, while the others are terminated with TAA (atp6, cox1, cox2, nad1, nad2, nad3, nad4l, nad5, and nad6), TAG (atp8) or AGA (cytb). The base composition is highly biased (34.9% A, 19.7% C, 11.9% G, and 33.5% T for the light strand) with an overall A + T content of 68.4%. Phylogenetic analysis indicated that M. miodon is more closely related to the consubfamilial long-eared hedgehog Hemiechinus auritus than to those within the order Eulipotyphla.

The mitochondrial genome of the Saunders's gull Chroicocephalus saundersi (Charadriiformes: Laridae) and a higher phylogeny of shorebirds (Charadriiformes)

The complete mitogenome of Chroicocephalus saundersi was characterized and compared with the 6 published Charadriiformes mitogenomes. The mitogenome of C. saundersi is a closed circular molecule 16,739 bp in size, and contains 37 genes and a control region. The AT and GC skews are positive and negative, respectively, and in agreement with those of the other Charadriiformes mitogenomes. The mitogenome of C. saundersi contains 3 start codons (ATG, GTG, and ATT), 4 stop codons (TAA, TAG, AGG, and AGA), and an incomplete stop codon (T-) in 13 PCGs. A codon usage analysis of all available Charadriiformes mitogenomes showed that the ATG (78%) and TAA (50.5%) were the most common start codon and stop codon, respectively. An unusual start codon, ATT, is commonly found in the ND3s of Charadriiformes mitogenomes, whereas the more common start codons, ATC and ATA, are rarely found. In all the Laridae species, one extra cytosine was inserted at position 174 in ND3. The control region of C. saundersi is 1180-bp long, with a nucleotide composition of 30.2% A, 28.6% T, 27.3% C, and 14.0% G. Variable numbers of tandem repeats (VNTRs) with nine copies of the 10 bp repeat sequence (AACAACAAAC) are found within the CSB domain of the control region. The ML/BI analyses, based on the amino acids of the 13 mitochondrial PCGs, strongly support the monophyly of the order Charadriiformes, with the suborder Lari considered sister to the Scolopaci, which is in turn a sister group to the suborder Charadrii.

The complete mitogenome of Hodgson's Red-Toothed Shrew, Episoriculus caudatus (Soricidae)

The Hodgson's Red-Toothed Shrew, Episoriculus caudatus belongs to the family Soricidae, and is widely distributed in northern South Asia, central and southern China and present in parts of northern Southeast Asia. In this study, the complete mitochondrial genome sequence of Episoriculus caudatus was determined. The mitogenome was 17,129 base pairs in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region, with a base composition of 33.1% A, 29.2% T, 24.7% C, and 13.0% G. The genome organization, nucleotide composition and codon usage did not differ significantly from those of other shrews. The study contributes to illuminating taxonomic status of Hodgson's Red-Toothed Shrew, Episoriculus caudatus.

The complete mitogenome of Chinese Mole Shrew, Anourosorex squamipes (Soricidae)

The Chinese Mole Shrew, Anourosorex squamipes belongs to the family Soricidae, and widely distributes in central and southern China, northern and south Burma, east India, northern Vietnam and Thailand. In this study, the complete mitochondrial genome sequence of Anourosorex squamipes was determined. The mitogenome is 17,121 base pairs in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region, with base composition of 34.0% A, 31.3% T, 22.0% C, and 12.7% G. The genome organization, nucleotide composition and codon usage did not differ significantly from those of other shrews. The study contributes to illuminating taxonomic status of Chinese Mole Shrew Anourosorex squamipes.

Superiority of a mechanistic codon substitution model even for protein sequences in phylogenetic analysis

Background

Nucleotide and amino acid substitution tendencies are characteristic of each species, organelle, and protein family. Hence, various empirical amino acid substitution rate matrices have needed to be estimated for phylogenetic analysis: JTT, WAG, and LG for nuclear proteins, mtREV for mitochondrial proteins, cpREV10 and cpREV64 for chloroplast-encoded proteins, and FLU for influenza proteins. On the other hand, in a mechanistic codon substitution model, in which each codon substitution rate is proportional to the product of a codon mutation rate and the ratio of fixation depending on the type of amino acid replacement, mutation rates and the strength of selective constraint on amino acids can be tailored to each protein family with additional 11 parameters. As a result, in the evolutionary analysis of codon sequences it outperforms codon substitution models equivalent to empirical amino acid substitution matrices. Is it superior even for amino acid sequences, among which synonymous substitutions cannot be identified?

Results

Nucleotide mutations are assumed to occur independently of codon positions but multiple nucleotide changes in infinitesimal time are allowed. Selective constraints on the respective types of amino acid replacements are tailored to each gene with a linear function of a given estimate of selective constraints, which were estimated by maximizing the likelihood of an empirical amino acid or codon substitution frequency matrix, each of JTT, WAG, LG, and KHG. It is shown that the mechanistic codon substitution model with the assumption of equal codon usage yields better values of Akaike and Bayesian information criteria for all three phylogenetic trees of mitochondrial, chloroplast, and influenza-A hemagglutinin proteins than the empirical amino acid substitution models with mtREV, cpREV64, and FLU, which were designed specifically for those protein families, respectively. The variation of selective constraint across sites fits the datasets significantly better than variable codon mutation rates, confirming that substitution rate variations across sites detected by amino acid substitution models are caused primarily by the variation of selective constraint against amino acid substitutions rather than the variation of codon mutation rate.

Conclusions

The mechanistic codon substitution model is superior to amino acid substitution models even in the evolutionary analysis of protein sequences.

Comparative Anatomy of the Bony Labyrinth (Inner Ear) of Placental Mammals

BACKGROUND

Variation is a naturally occurring phenomenon that is observable at all levels of morphology, from anatomical variations of DNA molecules to gross variations between whole organisms. The structure of the otic region is no exception. The present paper documents the broad morphological diversity exhibited by the inner ear region of placental mammals using digital endocasts constructed from high-resolution X-ray computed tomography (CT). Descriptions cover the major placental clades, and linear, angular, and volumetric dimensions are reported.

PRINCIPAL FINDINGS

The size of the labyrinth is correlated to the overall body mass of individuals, such that large bodied mammals have absolutely larger labyrinths. The ratio between the average arc radius of curvature of the three semicircular canals and body mass of aquatic species is substantially lower than the ratios of related terrestrial taxa, and the volume percentage of the vestibular apparatus of aquatic mammals tends to be less than that calculated for terrestrial species. Aspects of the bony labyrinth are phylogenetically informative, including vestibular reduction in Cetacea, a tall cochlear spiral in caviomorph rodents, a low position of the plane of the lateral semicircular canal compared to the posterior canal in Cetacea and Carnivora, and a low cochlear aspect ratio in Primatomorpha.

SIGNIFICANCE

The morphological descriptions that are presented add a broad baseline of anatomy of the inner ear across many placental mammal clades, for many of which the structure of the bony labyrinth is largely unknown. The data included here complement the growing body of literature on the physiological and phylogenetic significance of bony labyrinth structures in mammals, and they serve as a source of data for future studies on the evolution and function of the vertebrate ear.

Comparative morphology of the Papillae Linguales and their connective tissue cores in the tongue of the greater japanese shrew-mole, Urotrichus talpoides

The external morphology of the papillae linguales (papillae filiformes, papillae fungiformes and papillae vallatae) and their connective tissue cores (CTCs) of the greater Japanese shrew-mole (Urotrichus talpoides) were analysed by optical and scanning electron microscopy. Papillae filiformes were distributed over the dorsal surface of the apex linguae, and on the rostral and caudal regions of the corpus linguae but were less numerous in the mid-region. They were absent from the radix linguae. A pair of oval papillae vallatae was situated at the border between the corpus linguae and the radix linguae. Papillae foliatae were absent. The epithelial surface of each papilla filiformis consisted of a circular concavity, a ring-like wall and either a single thumb-like process or 2–3 slender pointed processes, depending on their location. The morphology of the CTCs of the papillae filiformes also varied regionally. The papillae linguales of the Japanese shrew-mole were morphologically similar to those of other Talpidae and Soricidae, including the common shrew, particularly with respect to the papillae filiformes in the mid- and caudal regions of the corpus linguae.

Advantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences

BACKGROUND

A mechanistic codon substitution model, in which each codon substitution rate is proportional to the product of a codon mutation rate and the average fixation probability depending on the type of amino acid replacement, has advantages over nucleotide, amino acid, and empirical codon substitution models in evolutionary analysis of protein-coding sequences. It can approximate a wide range of codon substitution processes. If no selection pressure on amino acids is taken into account, it will become equivalent to a nucleotide substitution model. If mutation rates are assumed not to depend on the codon type, then it will become essentially equivalent to an amino acid substitution model. Mutation at the nucleotide level and selection at the amino acid level can be separately evaluated.

RESULTS

The present scheme for single nucleotide mutations is equivalent to the general time-reversible model, but multiple nucleotide changes in infinitesimal time are allowed. Selective constraints on the respective types of amino acid replacements are tailored to each gene in a linear function of a given estimate of selective constraints. Their good estimates are those calculated by maximizing the respective likelihoods of empirical amino acid or codon substitution frequency matrices. Akaike and Bayesian information criteria indicate that the present model performs far better than the other substitution models for all five phylogenetic trees of highly-divergent to highly-homologous sequences of chloroplast, mitochondrial, and nuclear genes. It is also shown that multiple nucleotide changes in infinitesimal time are significant in long branches, although they may be caused by compensatory substitutions or other mechanisms. The variation of selective constraint over sites fits the datasets significantly better than variable mutation rates, except for 10 slow-evolving nuclear genes of 10 mammals. An critical finding for phylogenetic analysis is that assuming variable mutation rates over sites lead to the overestimation of branch lengths.

Molecular phylogeny of the higher and lower taxonomy of the Fusarium genus and differences in the evolutionary histories of multiple genes

BACKGROUND

Species of the Fusarium genus are important fungi which is associated with health hazards in human and animals. The taxonomy of this genus has been a subject of controversy for many years. Although many researchers have applied molecular phylogenetic analysis to examine the taxonomy of Fusarium species, their phylogenetic relationships remain unclear only few comprehensive phylogenetic analyses of the Fusarium genus and a lack of suitable nucleotides and amino acid substitution rates. A previous stugy with whole genome comparison among Fusairum species revealed the possibility that each gene in Fusarium genomes has a unique evolutionary history, and such gene may bring difficulty to the reconstruction of phylogenetic tree of Fusarium. There is a need not only to check substitution rates of genes but also to perform the exact evaluation of each gene-evolution.

RESULTS

We performed phylogenetic analyses based on the nucleotide sequences of the rDNA cluster region (rDNA cluster), and the β-tubulin gene (β-tub), the elongation factor 1α gene (EF-1α), and the aminoadipate reductase gene (lys2). Although incongruence of the tree topologies between lys2 and the other genes was detected, all genes supported the classification of Fusarium species into 7 major clades, I to VII. To obtain a reliable phylogeny for Fusarium species, we excluded the lys2 sequences from our dataset, and re-constructed a maximum likelihood (ML) tree based on the combined data of the rDNA cluster, β-tub, and EF-1α. Our ML tree indicated some interesting relationships in the higher and lower taxa of Fusarium species and related genera. Moreover, we observed a novel evolutionary history of lys2. We suggest that the unique tree topologies of lys2 are not due to an analytical artefact, but due to differences in the evolutionary history of genomes caused by positive selection of particular lineages.

CONCLUSION

This study showed the reliable species tree of the higher and lower taxonomy in the lineage of the Fusarium genus. Our ML tree clearly indicated 7 major clades within the Fusarium genus. Furthermore, this study reported differences in the evolutionary histories among multiple genes within this genus for the first time.

Adaptive evolution of energy metabolism genes and the origin of flight in bats

Bat flight poses intriguing questions about how flight independently developed in mammals. Flight is among the most energy-consuming activities. Thus, we deduced that changes in energy metabolism must be a primary factor in the origin of flight in bats. The respiratory chain of the mitochondrial produces 95% of the adenosine triphosphate (ATP) needed for locomotion. Because the respiratory chain has a dual genetic foundation, with genes encoded by both the mitochondrial and nuclear genomes, we examined both genomes to gain insights into the evolution of flight within mammals. Evidence for positive selection was detected in 23.08% of the mitochondrial-encoded and 4.90% of nuclear-encoded oxidative phosphorylation (OXPHOS) genes, but in only 2.25% of the nuclear-encoded nonrespiratory genes that function in mitochondria or 1.005% of other nuclear genes in bats. To address the caveat that the two available bat genomes are of only draft quality, we resequenced 77 OXPHOS genes from four species of bats. The analysis of the resequenced gene data are in agreement with our conclusion that a significantly higher proportion of genes involved in energy metabolism, compared with background genes, show evidence of adaptive evolution specific on the common ancestral bat lineage. Both mitochondrial and nuclear-encoded OXPHOS genes display evidence of adaptive evolution along the common ancestral branch of bats, supporting our hypothesis that genes involved in energy metabolism were targets of natural selection and allowed adaptation to the huge change in energy demand that were required during the origin of flight.

The new framework for understanding placental mammal evolution

An unprecedented level of confidence has recently crystallized around a new hypothesis of how living placental mammals share a pattern of common descent. The major groups are afrotheres (e.g., aardvarks, elephants), xenarthrans (e.g., anteaters, sloths), laurasiatheres (e.g., horses, shrews), and euarchontoglires (e.g., humans, rodents). Compared with previous hypotheses this tree is remarkably stable; however, some uncertainty persists about the location of the placental root, and (for example) the position of bats within laurasiatheres, of sea cows and aardvarks within afrotheres, and of dermopterans within euarchontoglires. A variety of names for sub-clades within the new placental mammal tree have been proposed, not all of which follow conventions regarding priority and stability. More importantly, the new phylogenetic framework enables the formulation of new hypotheses and testing thereof, for example regarding the possible developmental dichotomy that seems to distinguish members of the newly identified southern and northern radiations of living placental mammals.

Statistical comparison of nucleotide, amino acid, and codon substitution models for evolutionary analysis of protein-coding sequences

Statistical models for the evolution of molecular sequences play an important role in the study of evolutionary processes. For the evolutionary analysis of protein-coding sequences, 3 types of evolutionary models are available: 1) nucleotide, 2) amino acid, and 3) codon substitution models. Selecting appropriate models can greatly improve the estimation of phylogenies and divergence times and the detection of positive selection. Although much attention has been paid to the comparisons among the same types of models, relatively little attention has been paid to the comparisons among the different types of models. Additionally, because such models have different data structures, comparison of those models using conventional model selection criteria such as Akaike information criterion (AIC) or Bayesian information criterion (BIC) is not straightforward. Here, we suggest new procedures to convert models of the above-mentioned 3 types to 64-dimensional models with nucleotide triplet substitution. These conversion procedures render it possible to statistically compare the models of these 3 types by using AIC or BIC. By analyzing divergent and conserved interspecific mammalian sequences and intraspecific human population data, we show the superiority of the codon substitution models and discuss the advantages and disadvantages of the models of the 3 types.

Synonymous substitutions substantially improve evolutionary inference from highly diverged proteins

Codon-and amino acid-substitution models are widely used for the evolutionary analysis of protein-coding DNA sequences. Using codon models, the amounts of both nonsynonymous and synonymous DNA substitutions can be estimated. The ratio of these amounts represents the strength of selective pressure. Using amino acid models, the amount of nonsynonymous substitutions is estimated, but that of synonymous substitutions is ignored. Although amino acid models lose any information regarding synonymous substitutions, they explicitly incorporate the information for amino acid replacement, which is empirically derived from databases. It is often presumed that when the protein-coding sequences are highly divergent, synonymous substitutions might be saturated and the evolutionary analysis may be hampered by synonymous noise. However, there exists no quantitative procedure to verify whether synonymous substitutions can be ignored; therefore, amino acid models have been arbitrarily selected. In this study, we investigate the issue of a statistical comparison between codon-and amino acid-substitution models. For this purpose, we propose a new procedure to transform a 20-dimensional amino acid model to a 61-dimensional codon model. This transformation reveals that amino acid models belong to a subset of the codon models and enables us to test whether synonymous substitutions can be ignored by using the likelihood ratio. Our theoretical results and analyses of real data indicate that synonymous substitutions are very informative and substantially improve evolutionary inference, even when the sequences are highly divergent. Therefore, we note that amino acid models should be adopted only after carefully investigating and discarding the possibility that synonymous substitutions can reveal important evolutionary information.

Molecular phylogenetic study on the origin and evolution of Mustelidae

The family Mustelidae, which consists of Mustelinae, Lutrinae, Melinae, and Taxidiinae, is the largest family among Carnivora and is a highly diverse group. Recent molecular phylogenetic studies have clarified the phylogenetic relations among Mustelidae, but there remain several unresolved problems, particularly concerning the deep branchings. Whereas many studies support the monophyly of Mustelidae+Procyonidae among Musteloidea, the relations between Mustelidae+Procyonidae, Ailuridae, and Miphitidae are still unclear. To address these problems, we inferred a tree on the basis of the sequences of mitochondrial genomes and of multiple nuclear genes using the maximum likelihood method. Our results strongly support the hypothesis that the Taxidiinae branched at first, followed by the branching of the Melinae. After that, Mustelinae diversified, and Lutrinae evolved within Mustelinae. With respect to the deep branchings in Musteloidea, the Ailuridae/Mephitidae monophyly tree and the Mephitidae-basal tree are indistinguishable in log-likelihood score, and this problem remains unresolved.

Chromosome painting among Proboscidea, Hyracoidea and Sirenia: support for Paenungulata (Afrotheria, Mammalia) but not Tethytheria

Despite marked improvements in the interpretation of systematic relationships within Eutheria, particular nodes, including Paenungulata (Hyracoidea, Sirenia and Proboscidea), remain ambiguous. The combination of a rapid radiation, a deep divergence and an extensive morphological diversification has resulted in a limited phylogenetic signal confounding resolution within this clade both at the morphological and nucleotide levels. Cross-species chromosome painting was used to delineate regions of homology between Loxodonta africana (2n=56), Procavia capensis (2n=54), Trichechus manatus latirostris (2n=48) and an outgroup taxon, the aardvark (Orycteropus afer, 2n=20). Changes specific to each lineage were identified and although the presence of a minimum of 11 synapomorphies confirmed the monophyly of Paenungulata, no change characterizing intrapaenungulate relationships was evident. The reconstruction of an ancestral paenungulate karyotype and the estimation of rates of chromosomal evolution indicate a reduced rate of genomic repatterning following the paenungulate radiation. In comparison to data available for other mammalian taxa, the paenungulate rate of chromosomal evolution is slow to moderate. As a consequence, the absence of a chromosomal character uniting two paenungulates (at the level of resolution characterized in this study) may be due to a reduced rate of chromosomal change relative to the length of time separating successive divergence events.

Robust time estimation reconciles views of the antiquity of placental mammals

BACKGROUND

Molecular studies have reported divergence times of modern placental orders long before the Cretaceous-Tertiary boundary and far older than paleontological data. However, this discrepancy may not be real, but rather appear because of the violation of implicit assumptions in the estimation procedures, such as non-gradual change of evolutionary rate and failure to correct for convergent evolution.

METHODOLOGY/PRINCIPAL FINDINGS

New procedures for divergence-time estimation robust to abrupt changes in the rate of molecular evolution are described. We used a variant of the multidimensional vector space (MVS) procedure to take account of possible convergent evolution. Numerical simulations of abrupt rate change and convergent evolution showed good performance of the new procedures in contrast to current methods. Application to complete mitochondrial genomes identified marked rate accelerations and decelerations, which are not obtained with current methods. The root of placental mammals is estimated to be approximately 18 million years more recent than when assuming a log Brownian motion model. Correcting the pairwise distances for convergent evolution using MVS lowers the age of the root about another 20 million years compared to using standard maximum likelihood tree branch lengths. These two procedures combined revise the root time of placental mammals from around 122 million years ago to close to 84 million years ago. As a result, the estimated distribution of molecular divergence times is broadly consistent with quantitative analysis of the North American fossil record and traditional morphological views.

CONCLUSIONS/SIGNIFICANCE

By including the dual effects of abrupt rate change and directly accounting for convergent evolution at the molecular level, these estimates provide congruence between the molecular results, paleontological analyses and morphological expectations. The programs developed here are provided along with sample data that reproduce the results of this study and are especially applicable studies using genome-scale sequence lengths.

Zoo-FISH in the European mole (Talpa europaea) detects all ancestral Boreo-Eutherian human homologous chromosome associations

Zoo-FISH with human whole-chromosome paint probes delineated syntenic association of human homologous chromosome segments 3-21, 14-15, 16-19, 4-8, 7-16 and 12-22 (twice) in the European mole (Talpa europaea, Talpidae, Eulipotyphla, Mammalia). These segment associations represent shared ancestral Boreo-Eutherian traits, half of which were previously not described for Eulipotyphla. The karyotype of the European mole acquired a minimum of 19 translocations and six inversions compared to the presumed Boreo-Eutherian ancestor.

Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions

Despite the recent large-scale efforts dedicated to comprehensive phylogenetic analyses using mitochondrial and nuclear DNA sequences, several relationships among mammalian orders remain controversial. Here, we present an extensive application of retroposon (L1) insertion analysis to the phylogenetic relationships among almost all mammalian orders. In addition to demonstrating the validity of Glires, Euarchontoglires, Laurasiatheria, and Boreoeutheria, we demonstrate an interordinal clade that links Chiroptera, Carnivora, and Perissodactyla within Laurasiatheria. Re-examination of a large DNA sequence data set yielded results consistent with our conclusion. We propose a superordinal name "Pegasoferae" for this clade of Chiroptera + Perissodactyla + Carnivora + Pholidota. The presence of a single incongruent L1 locus generates a tree in which the group of Carnivora + Perissodactyla associates with Cetartiodactyla but not with Chiroptera. This result suggests that incomplete lineage sorting of an ancestral dimorphism occurred with regard to the presence or absence of retroposon alleles in a common ancestor of Scrotifera (Pegasoferae + Cetartiodactyla), which was followed by rapid divergence into the extant orders over an evolutionarily short period. Accordingly, Euungulata (Cetartiodactyla + Perissodactyla) and Fereuungulata (Carnivora + Pholidota + Perissodactyla + Cetartiodactyla) cannot be validated as natural groups. The interordinal mammalian relationships presented here provide a cornerstone for future studies in the reconstruction of mammalian classifications, including extinct species, on evolution of large genomic sequences and structure, and in developmental analysis of morphological diversification.

New candidate species most closely related to penguins

The phylogenetic position of the order Spenisciformes in Aves remains unclear despite several independent analyses based on morphological and molecular data. To address this issue, we determined the complete mtDNA sequence of rockhopper penguins. The mitochondrial genome, excluding the region from the D-loop to 12SrRNA, was also sequenced for petrel, albatross, frigatebird, loon and grebe, which previous studies suggest are related to penguins. A maximum likelihood analysis of the phylogenetic placement of penguins with 23 birds, including 17 species whose mtDNA sequences were previously reported, suggested that storks are the closest extant relatives of penguins, with 78% and 56% bootstrap supports, depending on the choice of outgroup species. Thus, ciconiiform birds constitute new candidates as the closest extant relatives of penguins (previously proposed candidates were either gaviiform, podicipediform, or procellariiform birds). In addition to this new evidence, our analysis gave evidence to some of ambiguous relationships in the avian tree: our analysis supported a basal split between passerines and other neoavians within Neoaves, and rejected the monophyly of Falconiformes as well as that of loons and grebes.

On the phylogenetic position of a rare Iberian endemic mammal, the Pyrenean desman (Galemys pyrenaicus)

The nucleotide sequences of the complete mitochondrial genome and nine partial nuclear genes of the Pyrenean desman (Galemys pyrenaicus) were determined in order to establish the relative phylogenetic position of this species at different taxonomic levels within the placental tree. Phylogenetic relationships of desman within the family Talpidae were inferred based on complete mitochondrial cytochrome b gene nucleotide sequence data. The Pyrenean desman was unambiguously recovered as sister group of the Russian desman (Desmana moschata) confirming the monophyly of the subfamily Desmaninae. However, phylogenetic relationships among major lineages within the Talpidae could not be confidently resolved. Phylogenetic analyses based on mitochondrial (at the amino acid level) and nuclear (at the nucleotide level) sequence data sets confidently placed desman within the Eulipotyphla (that also included moles, shrews, and hedgehogs), and partially recovered placental interordinal relationships. The monophyly of Laurasiatheria (including Eulipotyphla, Chiroptera, Carnivora, Pholidota, Perissodactyla, and Cetartiodactyla) was strongly supported. Mitochondrial amino acid sequences of Pholidota (pangolins) were found to bias phylogenetic inferences due to long-branch attraction effects. A Bayesian inference based on a combined mitochondrial and nuclear data set without Pholidota arrived at an almost fully resolved tree that supported the basal position of Eulipotyphla within Laurasiatheria.

Cross-species chromosome painting unveils cytogenetic signatures for the Eulipotyphla and evidence for the polyphyly of Insectivora

Insectivore-like animals are traditionally believed among the first eutherian mammals that have appeared on the earth. The modern insectivores are thus crucial for understanding the systematics and phylogeny of eutherian mammals as a whole. Here cross-species chromosome painting, with probes derived from flow-sorted chromosomes of human, was used to delimit the homologous chromosomal segments in two Soricidae species, the common shrew (Sorex araneus, 2n = 20/21), and Asiatic short-tailed shrew (Blarinella griselda, 2n = 44), and one Erinaceidae species, the shrew-hedgehog (Neotetracus sinensis, 2n = 32), and human. We report herewith the first comparative maps for the Asiatic short-tailed shrew and the shrew-hedgehog, in addition to a refined comparative map for the common shrew. In total, the 22 human autosomal paints detected 40, 51 and 58 evolutionarily conserved segments in the genomes of common shrew, Asiatic short-tailed shrew, and shrew-hedgehog, respectively, demonstrating that the common shrew has retained a conserved genome organization while the Asiatic short-tailed shrew and shrew-hedgehog have relatively rearranged genomes. In addition to confirming the existence of such ancestral human segmental combinations as HSA 3/21, 12/22, 14/15 and 7/16 that are shared by most eutherian mammals, our study reveals a shared human segmental combination, HSA 4/20, that could phylogenetically unite the Eulipotyphlan (i.e., the core insectivores) species. Our results provide cytogenetic evidence for the polyphyly of the order Insectivora and additional data for the eventual reconstruction of the ancestral eutherian karyotype.

Phylogeny and life histories of the 'Insectivora': controversies and consequences

The evolutionary relationships of the eutherian order Insectivora (Lipotyphla sensu stricto) are the subject of considerable debate. The difficulties in establishing insectivore phylogeny stem from their lack of many shared derived characteristics. The grouping is therefore something of a 'wastebasket' taxon. Most of the older estimates of phylogeny, based on morphological evidence, assumed insectivore monophyly. More recently, molecular phylogenies argue strongly against monophyly, although they differ in the extent of polyphyly inferred for the order. I review the history of insectivore phylogenetics and systematics, focussing on the relationships between the six extant families (Erinaceidae--hedgehogs and moonrats, Talpidae - moles and desmans, Soricidae - shrews, Solenodontidae--solenodons, Tenrecidae--tenrecs and otter-shrews and Chrysochloridae--golden moles). I then examine how these various phylogenetic hypotheses influence the results of comparative analyses and our interpretation of insectivore life-history evolution. I assess which particular controversies have the greatest effect on results, and discuss the implications for comparative analyses where the phylogeny is controversial. I also explore and suggest explanations for certain insectivore life-history trends: increased gestation length and litter size in tenrecs, increased encephalization in moles, and the mixed fast and slow life-history strategies in solenodons. Finally, I consider the implications for comparative analyses of the recent strongly supported phylogenetic hypothesis of an endemic African clade of mammals that includes the insectivore families of tenrecs and golden moles.

Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data

Because of the increase of genomic data, multiple genes are often available for the inference of phylogenetic relationships. The simple approach for combining multiple genes from the same taxon is to concatenate the sequences and then ignore the fact that different positions in the concatenated sequence came from different genes. Here, we discuss two criteria for inferring the optimal tree topology from data sets with multiple genes. These criteria are designed for multigene data sets where gene-specific evolutionary features are too important to ignore. One criterion is conventional and is obtained by taking the sum of log-likelihoods over all genes. The other criterion is obtained by dividing the log-likelihood for a gene by its sequence length and then taking the arithmetic mean over genes of these ratios. A similar strategy could be adopted with parsimony scores. The optimal tree is then declared to be the one for which the sum or the arithmetic mean is maximized. These criteria are justified within a two-stage hierarchical framework. The first level of the hierarchy represents gene-specific evolutionary features, and the second represents site-specific features for given genes. For testing significance of the optimal topology, we suggest a two-stage bootstrap procedure that involves resampling genes and then resampling alignment columns within resampled genes. An advantage of this procedure over concatenation is that it can effectively account for gene-specific evolutionary features. We discuss the applicability of the two-stage bootstrap idea to the Kishino-Hasegawa test and the Shimodaira-Hasegawa test.

Multidimensional vector space representation for convergent evolution and molecular phylogeny

With growing amounts of genome data and constant improvement of models of molecular evolution, phylogenetic reconstruction became more reliable. However, our knowledge of the real process of molecular evolution is still limited. When enough large-sized data sets are analyzed, any subtle biases in statistical models can support incorrect topologies significantly because of the high signal-to-noise ratio. We propose a procedure to locate sequences in a multidimensional vector space (MVS), in which the geometry of the space is uniquely determined in such a way that the vectors of sequence evolution are orthogonal among different branches. In this paper, the MVS approach is developed to detect and remove biases in models of molecular evolution caused by unrecognized convergent evolution among lineages or unexpected patterns of substitutions. Biases in the estimated pairwise distances are identified as deviations (outliers) of sequence spatial vectors from the expected orthogonality. Modifications to the estimated distances are made by minimizing an index to quantify the deviations. In this way, it becomes possible to reconstruct the phylogenetic tree, taking account of possible biases in the model of molecular evolution. The efficacy of the modification procedure was verified by simulating evolution on various topologies with rate heterogeneity and convergent change. The phylogeny of placental mammals in previous analyses of large data sets has varied according to the genes being analyzed. Systematic deviations caused by convergent evolution were detected by our procedure in all representative data sets and were found to strongly affect the tree structure. However, the bias correction yielded a consistent topology among data sets. The existence of strong biases was validated by examining the sites of convergent evolution between the hedgehog and other species in mitochondrial data set. This convergent evolution explains why it has been difficult to determine the phylogenetic placement of the hedgehog in previous studies.

Indels in protein-coding sequences of Euarchontoglires constrain the rooting of the eutherian tree

Despite the availability of large molecular data sets, the position of the root of the eutherian tree remains a controversial issue. Depending on source data, taxon sampling and analytical approach, the root can be placed at either Afrotheria, Xenarthra, Afrotheria+Xenarthra, or murid rodents. We explored the phylogenetic potential of indels in four nuclear protein-coding genes (SCA1, PRNP, TNFalpha, and HspB3) with regard to a possible rooting at the murid branch. According to parsimony principles, five indels were interpreted to contradict such a rooting, and one indel to support it. The results illustrate that indels, despite the occurrence of homoplasy, can be convincing sources of independent molecular evidence to distinguish between alternative phylogenetic hypotheses.