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PubMed1996

Evolution of eutherian cytochrome c oxidase subunit II: heterogeneous rates of protein evolution and altered interaction with cytochrome c.

Cytochrome c oxidase subunit II (COII), encoded by the mitochondrial genome, exhibits one of the most heterogeneous rates of amino acid replacement among placental mammals. Moreover, it has been demonstrated that cytochrome c oxidase has undergone a structural change in higher primates which has altered its physical interaction with cytochrome c. We collected a large data set of COII sequences from several orders of mammals with emphasis on primates, rodents, and artiodactyls. Using phylogenetic hypotheses based on data independent of the COII gene, we demonstrated that an increased number of amino acid replacements are concentrated among higher primates. Incorporating approximate divergence dates derived from the fossil record, we find that most of the change occurred independently along the New World monkey lineage and in a rapid burst before apes and Old World monkeys diverged. There is some evidence that Old World monkeys have undergone a faster rate of nonsynonymous substitution than have apes. Rates of substitution at four-fold degenerate sites in primates are relatively homogeneous, indicating that the rate heterogeneity is restricted to nondegenerate sites. Excluding the rate acceleration mentioned above, primates, rodents, and artiodactyls have remarkably similar nonsynonymous replacement rates. A different pattern is observed for transversions at four-fold degenerate sites, for which rodents exhibit a higher rate of replacement than do primates and artiodactyls. Finally, we hypothesize specific amino acid replacements which may account for much of the structural difference in cytochrome c oxidase between higher primates and other mammals.

Amino Acids↗

PubMed2006

Molecular phylogenetics of the exoneurine allodapine bees reveal an ancient and puzzling dispersal from Africa to Australia.

Previous phylogenetic studies of the bee tribe Allodapini suggested a puzzling biogeographic problem: one of the key basal divergences involved separation of the southern African and southern Australian clades at a very early stage in allodapine evolution, but no taxa occur in the Palaearctic or Asian regions that might suggest a Laurasian dispersal route. However, these studies lacked sufficient sequence data and appropriate maximum likelihood partition models to provide reliable phylogenetic estimates and enable alternative biogeographic hypotheses to be distinguished. Using Bayesian and penalized likelihood approaches and an expanded sequence and taxon set we examine phylogenetic relationships between the Australian, African, and Malagasy groups and estimate divergence times for key nodes. We show that divergence of the three basal Australian clades (known as the exoneurines) occurred at least 25 Mya following a single colonization event, and that this group diverged from the African + Madagascan clade at least 30 Mya, but actual divergence dates are likely to be much older than these very conservative limits. The bifurcation order of the exoneurine clades was not resolved and analyses could not rule out the existence of a hard polytomy, suggesting rapid radiation after colonization of Australia. Their divergence involved major transitions in life history traits and these placed constraints on the kinds of social organization that subsequently evolved in each lineage. Early divergence between the African, Malagasy, and Australian clades presents a major puzzle for historical biogeography: node ages are too recent for Gondwanan vicariance hypotheses, but too early for Laurasian dispersal scenarios. We suggest a scenario involving island hopping across the Indian Ocean via a series of now largely submerged elements of the Kergulen Plateau and Broken Ridge provinces, both of which are known to have had subaerial formations during the Cenozoic. [Bayesian; biogeography; dispersal; Gondwana; Kerguelen Plateau; penalized likelihood.].

Africa↗

PubMed2001

Aldehyde dehydrogenase gene superfamily: the 2000 update.

Aldehyde dehydrogenase (ALDH) superfamily represents a group of NAD(P)(+)-dependent enzymes that catalyze the oxidation of a wide spectrum of endogenous and exogenous aldehydes. With the advent of megabase genome sequencing, the ALDH superfamily is expanding rapidly on many fronts. As expected, ALDH genes are found in virtually all genomes analyzed to date, indicating the importance of these enzymes in biological functions. Complete genome sequences of various species have revealed additional ALDH genes. As of July 2000, the ALDH superfamily consists of 331 distinct genes, of which eight are found in archaea, 165 in eubacteria, and 158 in eukaryota. The number of ALDH genes in some species with their genomes completely sequenced and annotated, Escherichia coli and Caenorhabditis elegans, ranges from 10 to 17. In the human genome, 17 functional genes and three pseudogenes have been identified to date. Divergent evolution, based on multiple alignment analysis of 86 eukaryotic ALDH amino-acid sequences, was the basis of the standardized ALDH gene nomenclature system (Pharmacogenetics 9: 421-434, 1999). Thus far, the eukaryotic ALDHs comprise 20 gene families. A complete list of all ALDH sequences known to date is presented here along with the evolution analysis of the eukaryotic ALDHs.

Aldehyde Dehydrogenase↗

PubMed1998

Evolution and phylogenetic utility of the period gene in Lepidoptera.

Evolution and phylogenetic utility of the period gene are explored through sequence analysis of a relatively conserved 909-bp fragment in 26 lepidopteran species. Taxa range from tribes to superfamilies, primarily within the putative clade Macrolepidotera plus near outgroups, and include both strongly established and problematic groupings. Their divergence dates probably range from the late Cretaceous through much of the Tertiary. Comparisons within the same set of closely related species show that amino acid substitutions in period occur 4.9 and 44 times as frequently as they do in two other nuclear genes--dopa decarboxylase and elongation factor-1 alpha, respectively. In contrast, rates of observed synonymous substitution are within 60% of each other for these three genes. Synonymous changes in period approach saturation by the family level, whereas nonsynonymous and amino acid divergences across the Macrolepidoptera are less than half the maximal values reported for this gene. Phylogenetic analyses of period strongly supported groupings at the family level and below. In contrast to previous analyses at this level with other nuclear genes, much of the information lies in nonsynonymous change. Relationships up to the superfamily level were recovered with decreasing effectiveness, and little, if any, signal was apparent regarding relationships among superfamilies. This could reflect rapid radiation of the superfamilies, however, rather than saturation in the period locus; thus, period, in combination with other genes, remains a plausible candidate for approaching the difficult problems of lepidopteran family and superfamily relationships.

Amino Acid Sequence↗

PubMed2002

Phylogenetics and evolution of the eastern Asian-eastern North American disjunct aphid tribe, Hormaphidini (Hemiptera: Aphididae).

A conspicuous biogeographic pattern of the Northern Hemisphere is the disjunct occurrence of related taxa on different continents. Perhaps best studied in plants, this pattern includes disjunct distributions of genera in eastern Asia and eastern North America. Such continental disjunctions are thought to be the remnants of a mostly continuously distributed, mixed mesophytic forest dating to the Miocene, which subsequently became fragmented by geological and climatic changes. Some highly host-specific insects, namely aphids, live on descendants of the mixed mesophytic forest taxa and exhibit the same disjunct distributions as that of their host plants. We estimated the phylogeny of Hormaphidini aphids, which host-alternate between witch-hazel (Hamamelis; an eastern Asian-eastern North American disjunct genus) and birch (Betula). Based on partial nuclear elongation factor 1alpha and mitochondrial tRNA leucine/cytochrome oxidase II sequences, trees inferred from maximum-parsimony and maximum-likelihood showed strong support for two monophyletic genera (Hamamelistes and Hormaphis), each containing a clade of Japanese and a clade of North American species. The estimated divergence dates of Asian and North American clades in both genera was 20-30 million years ago, consistent with the idea that aphids may have experienced the same vicariance events as those of their host plants.

Animals↗

PubMed2006

Testing the molecular clock: molecular and paleontological estimates of divergence times in the Echinoidea (Echinodermata).

The phylogenetic relationships of 46 echinoids, with representatives from 13 of the 14 ordinal-level clades and about 70% of extant families commonly recognized, have been established from 3 genes (3,226 alignable bases) and 119 morphological characters. Morphological and molecular estimates are similar enough to be considered suboptimal estimates of one another, and the combined data provide a tree that, when calibrated against the fossil record, provides paleontological estimates of divergence times and completeness of their fossil record. The order of branching on the cladogram largely agrees with the stratigraphic order of first occurrences and implies that their fossil record is more than 85% complete at family level and at a resolution of 5-Myr time intervals. Molecular estimates of divergence times derived from applying both molecular clock and relaxed molecular clock models are concordant with estimates based on the fossil record in up to 70% of cases, with most concordant results obtained using Sanderson's semiparametric penalized likelihood method and a logarithmic-penalty function. There are 3 regions of the tree where molecular and fossil estimates of divergence time consistently disagree. Comparison with results obtained when molecular divergence dates are estimated from the combined (morphology + gene) tree suggests that errors in phylogenetic reconstruction explain only one of these. In another region the error most likely lies with the paleontological estimates because taxa in this region are demonstrated to have a very poor fossil record. In the third case, morphological and paleontological evidence is much stronger, and the topology for this part of the molecular tree differs from that derived from the combined data. Here the cause of the mismatch is unclear but could be methodological, arising from marked inequality of molecular rates. Overall, the level of agreement reached between these different data and methodological approaches leads us to believe that careful application of likelihood and Bayesian methods to molecular data provides realistic divergence time estimates in the majority of cases (almost 80% in this specific example), thus providing a remarkably well-calibrated phylogeny of a character-rich clade of ubiquitous marine benthic invertebrates.

Animals↗

PubMed2006

The pattern and timing of diversification of Philippine endemic rodents: evidence from mitochondrial and nuclear gene sequences.

The 22 genera and 64 species of rodents (Muridae: Murinae) distributed in the Philippine Islands provide a unique opportunity to study patterns and processes of diversification in island systems. Over 90% of these rodent species are endemic to the archipelago, but the relative importance of dispersal from the mainland, dispersal within the archipelago, and in situ differentiation as explanations of this diversity remains unclear, as no phylogenetic hypothesis for these species and relevant mainland forms is currently available. Here we report the results of phylogenetic analyses of the endemic Philippine murines and a wide sampling of murine diversity from outside the archipelago, based on the mitochondrial cytochrome b gene and the nuclear-encoded IRBP exon 1. Analysis of our combined gene data set consistently identified five clades comprising endemic Philippine genera, suggesting multiple invasions of the archipelago. Molecular dating analyses using parametric and semiparametric methods suggest that colonization occurred in at least two stages, one ca. 15 Mya, and another 8 to 12 million years later, consistent with the previous recognition of "Old" and "New" endemic rodent faunas. Ancestral area analysis suggests that the Old Endemics invaded landmasses that are now part of the island of Luzon, whereas the three New Endemic clades may have colonized through either Mindanao, Luzon, or both. Further, our results suggest that most of the diversification of Philippine murines took place within the archipelago. Despite heterogeneity between nuclear and mitochondrial genes in most model parameters, combined analysis of the two data sets using both parsimony and likelihood increased phylogenetic resolution; however, the effect of data combination on support for resolved nodes was method dependent. In contrast, our results suggest that combination of mitochondrial and nuclear data to estimate relatively ancient divergence times can severely compromise those estimates, even when specific methods that account for rate heterogeneity among genes are employed. [Biogeography; divergence date estimation; mitochondrial DNA; molecular systematics; Murinae; nuclear exon; Philippines; phylogeny.].

Animals↗

PubMed2003

Time flies, a new molecular time-scale for brachyceran fly evolution without a clock.

The insect order Diptera, the true flies, contains one of the four largest Mesozoic insect radiations within its suborder Brachycera. Estimates of phylogenetic relationships and divergence dates among the major brachyceran lineages have been problematic or vague because of a lack of consistent evidence and the rarity of well-preserved fossils. Here, we combine new evidence from nucleotide sequence data, morphological reinterpretations, and fossils to improve estimates of brachyceran evolutionary relationships and ages. The 28S ribosomal DNA (rDNA) gene was sequenced for a broad diversity of taxa, and the data were combined with recently published morphological scorings for a parsimony-based phylogenetic analysis. The phylogenetic topology inferred from the combined 28S rDNA and morphology data set supports brachyceran monophyly and the monophyly of the four major brachyceran infraorders and suggests relationships largely consistent with previous classifications. Weak support was found for a basal brachyceran clade comprising the infraorders Stratiomyomorpha (soldier flies and relatives), Xylophagomorpha (xylophagid flies), and Tabanomorpha (horse flies, snipe flies, and relatives). This topology and similar alternative arrangements were used to obtain Bayesian estimates of divergence times, both with and without the assumption of a constant evolutionary rate. The estimated times were relatively robust to the choice of prior distributions. Divergence times based on the 28S rDNA and several fossil constraints indicate that the Brachycera originated in the late Triassic or earliest Mesozoic and that all major lower brachyceran fly lineages had near contemporaneous origins in the mid-Jurassic prior to the origin of flowering plants (angiosperms). This study provides increased resolution of brachyceran phylogeny, and our revised estimates of fly ages should improve the temporal context of evolutionary inferences and genomic comparisons between fly model organisms.

Animals↗

PubMed2005

Genetic diversity and historical demography of Atlantic bigeye tuna (Thunnus obesus).

Bigeye (Thunnus obesus) is a large, pelagic, and migratory species of tuna that inhabits tropical and temperate marine waters worldwide. Previous studies based on mitochondrial RFLP data have shown that bigeye tunas from the Atlantic Ocean are the most interesting from a genetic point of view. Two highly divergent mitochondrial haplotype clades (I and II) coexist in the Atlantic Ocean. One is almost exclusive of the Atlantic Ocean whereas the other is also found in the Indo-Pacific Ocean. Bigeye tuna from the Atlantic Ocean is currently managed as a single stock, although this assumption remains untested at the genetic level. Therefore, genetic diversity was determined at the mitochondrial control region to test the null hypothesis of no population structure in bigeye tuna from the Atlantic Ocean. A total of 331 specimens were sampled from four locations in the Atlantic Ocean (Canada, Azores, Canary Islands, and Gulf of Guinea), and one in the Indian and Pacific Oceans, respectively. The reconstructed neighbor-joining phylogeny confirmed the presence of Clades I and II throughout the Atlantic Ocean. No apparent latitudinal gradient of the proportions of both clades in the different collection sites was observed. Hierarchical AMOVA tests and pairwise phi(ST) comparisons involving Atlantic Ocean Clades I and II were consistent with a single stock of bigeye tuna in the Atlantic Ocean. Population genetic analyses considering phylogroups independently supported gene flow within Clade II throughout the Atlantic Ocean, and within Clade I between Atlantic and Indo-Pacific Oceans. The latter result suggests present uni-directional gene flow from the Indo-Pacific into the Atlantic Ocean. Moreover, mismatch analyses dated divergence of Clades I and II during the Pleistocene, as previously proposed. In addition, migration rates were estimated using coalescent methods, and showed a net migration from Atlantic Ocean feeding grounds towards the Gulf of Guinea, the best-known spawning ground of Atlantic bigeye tuna.

Animals↗

PubMed1989

Only DFL16, DSP2, and DQ52 gene families exist in mouse immunoglobulin heavy chain diversity gene loci, of which DFL16 and DSP2 originate from the same primordial DH gene.

In mice, 12 germ-line DH genes belonging to three different families (DQ52, DSP2 and DFL16) have been identified. The DH genes other than DQ52 are clustered in the 60 kb-long region located between VH and JH genes. Since there are seven DH gene families (DHQ52, DXP, DA, DK, DN, DM and DLR) in humans, we tried to identify new DH gene families in the 60 kb-long region using human DH gene probes. Mouse and human DH genes showing the highest similarity were mouse DFL16 genes and human DA genes. Southern hybridization of the mouse clones covering the 60-kb region with human DH probes did not detect any other DH genes. Nucleotide sequence analysis of the 4.0-kb fragment containing the DFL16.1 gene confirmed this conclusion. Comparison of the 12 germ-line DH genes and more than 150 somatic DH sequences also indicated that there are not more germ-line DH genes in the mouse genome. Moreover, comparison of nucleotide sequences of DFL16.1 and DSP2.2 genes and their surrounding regions suggests that both DH gene families originate from the same primordial DH gene. Using the flanking sequences of both DH genes, the divergence date between DFL16 and DSP2 genes was estimated at around 37 million years ago.

Animals↗

PubMed1996

A new approach to studying modern human origins: hypothesis testing with coalescence time distributions.

A new approach for testing hypotheses about modern human origins using molecular divergence dates is presented. Coalescence times from many unlinked loci are needed to test the alternative models. Hypotheses are evaluated on the basis of their differing predicted distribution patterns of coalescence times from multiple genes. No single coalescence time from one genetic system is sufficient to reject any of the three alternative models. Several nuclear datasets give recent dates for human genetic ancestors, at approximately the mitochondrial coalescence time, while some nuclear datasets support older dates. Given the overall distribution of available mitochondrial and nuclear coalescence times, the rapid replacement hypothesis is the likeliest model for modern human origins. The unusual nature of the human mitochondrial pattern is highlighted by comparative data from nonhuman hominoids. To understand the pattern of modern human genetic variability better, more nuclear data from all hominoid species are needed.

Animals↗

PubMed1998

What does palaeontology contribute to systematics in a molecular world?

Palaeontology provides the only direct record for morphological and genetic change through time and uniquely contributes to systematics in two ways: by providing access to denser taxon sampling than is otherwise possible and by dating divergence times. Claims that ancient DNA has survived millions of years in certain fossils suggested the possibility that palaeontology could contribute directly to molecular systematic studies. Unfortunately, none of the supposed geologically ancient DNA records stands up to detailed scrutiny and fossils therefore contribute primarily through the morphological information they preserve. Denser taxon sampling can improve the accuracy of phylogenetic estimates primarily through allowing better discrimination of homoplasy from homology. This in turn leads to more accurate hypotheses of character transformation. Denser taxon sampling also offers the opportunity for more accurate rooting, since more characters can be polarized by reference to a stem-group taxon than to an extant sister-group taxon. Missing data can be a problem for fossils, but is not crippling. Finally the temporal order of clade appearances in the fossil record can provide ancillary evidence for selecting a working phylogeny from among a number of equally most parsimonious cladograms.

Animals↗

PubMed1999

Molecular phylogeny and evolution of Sorex shrews (Soricidae: insectivora) inferred from mitochondrial DNA sequence data.

Shrews of the genus Sorex are characterized by a Holarctic distribution, and relationships among extant taxa have never been fully resolved. Phylogenies have been proposed based on morphological, karyological, and biochemical comparisons, but these analyses often produced controversial and contradictory results. Phylogenetic analyses of partial mitochondrial cytochrome b gene sequences (1011 bp) were used to examine the relationships among 27 Sorex species. The molecular data suggest that Sorex comprises two major monophyletic lineages, one restricted mostly to the New World and one with a primarily Palearctic distribution. Furthermore, several sister-species relationships are revealed by the analysis. Based on the split between the Soricinae and Crocidurinae subfamilies, we used a 95% confidence interval for both the calibration of a molecular clock and the subsequent calculation of major diversification events within the genus Sorex. Our analysis does not support an unambiguous acceleration of the molecular clock in shrews, the estimated rate being similar to other estimates of mammalian mitochondrial clocks. In addition, the data presented here indicate that estimates from the fossil record greatly underestimate divergence dates among Sorex taxa.

Animals↗

PubMed2001

From the Old World to the New World: a molecular chronicle of the phylogeny and biogeography of hystricognath rodents.

Hystricognath rodents include Old World Phiomorpha and New World Caviomorpha. These two groups have an enigmatic biogeographical history. Using a nuclear marker, the exon 28 of the von Willebrand Factor gene (vWF), we reconstructed the phylogenetic relationships among 23 Hystricognathi species. These taxa encompass the complete familial diversity of the Hystricognathi. Our results indicate a basal trifurcation of hystricognaths leading to Hystricidae, Phiomorpha s.s. (Bathyergidae, Thryonomyidae, and Petromuridae), and Caviomorpha. The monophyly of caviomorphs is robustly supported, confirming a single colonization event of South America by hystricognaths. Caviomorpha are divided into four lineages: Cavioidea, Erethizontoidea, Chinchilloidea, and Octodontoidea. Furthermore, we suggest that (1) Chinchillidae and Dinomyidae are sister clades, (2) Abrocomidae is a true Octodontoidea, and (3) Capromyidae, Echimyidae, and Myocastoridae cluster together. Surprisingly, Erethizontidae does not appear to be the most diverged caviomorph lineage. The molecular results are discussed in the light of previous paleontological and morphological observations. Local molecular clocks are used to estimate divergence dates among hystricognath lineages. An Asian origin is suggested for Caviomorpha, and a colonization route through Australia and Antarctica is indicated as an alternative to the hypothesis of a transatlantic migration of Caviomorpha from Africa to South America.

Animals↗

PubMed2002

Molecular systematics of sciurognathi (rodentia): the mitochondrial cytochrome b and 12S rRNA genes support the Anomaluroidea (Pedetidae and Anomaluridae).

Nucleotide sequence data from the mitochondrial 12S rRNA and cytochrome b genes were used to analyze phylogenetic relationships among sciurognath rodents. Our sample taxa included representatives of 11 sciurognath and 3 hystricognath families with two marsupial species, Didelphis virginiana and Macropus robustus, as outgroups. The dataset was analyzed using both maximum-parsimony (weighted and unweighted) and likelihood methods. Three suprafamilial groupings are strongly supported: Geomyidae + Heteromyidae (Geomyoidea), Sciuridae + Aplodontidae (Sciuroidea), and Pedetidae + Anomaluridae (Anomaluroidea). Although moderately supported, two sister group relationships were identified between Gliridae and Sciuroidea and between Castor and Geomyoidea. In contrast to previous nuclear DNA evidence, the evolutionary affinities between Ctenodactylidae and Hystricognathi (Ctenohystrica) and between Muridae and Dipodidae (Myodonta) are not supported by the mitochondrial data. Molecular divergence dates based on the combined data were estimated for suprafamilial groupings and are discussed in the light of current morphological and paleontological interpretations of rodent phylogeny.

Animals↗

PubMed1998

Variable substitution rates of the 18 domain sequences in Artemia hemoglobin.

The Artemia hemoglobin is a dimer comprising two nine-domain covalent polymers in quaternary association. Each polymer is encoded by a gene representing nine successive globin domains which have different sequences and are presumed to have been copied originally from a single-domain gene. Two different polymers exist as the result of a complete duplication of the nine-domain gene, allowing the formation of either homodimers or the heterodimer. The total population size of 18 domains comprising nine corresponding pairs, coupled with the probability that they reflect several hundred million years of evolution in the same lineage, provides a unique model in which the process of gene multiplication can be analyzed. The outcome has important implications for the reliability of local molecular clocks. The two polymers differ from each other at 11.7% of amino acid sites; however when corresponding individual domains are compared between polymers, amino acid substitution fluctuates by a factor of 2.7-fold from lowest to highest. This variation is not obvious at the DNA level: Domain pair identity values fluctuate by 1. 3-fold. Identity values are, however, uncorrected for multiple substitutions, and both silent and nonsilent changes are pooled. Therefore, to determine the variability in relative substitution rates at the DNA level, we have used the method of Li (1993, J Mol Evol 36:96-99) to determine estimates of nonsynonymous (KA) and synonymous (KS) substitutions per site for the nine pairs of domains. As expected, the overall level of silent substitutions (KS of 56. 9%) far exceeded nonsilent substitutions (KA of 6.7%); however, for corresponding domain pairs, KA fluctuates by 2.3-fold and KS by 1. 7-fold. The large discrepancies reflected in the expressed protein have accrued within a single lineage and the implication is that divergence dates of different genera based on amino acid sequences, even with well-studied proteins of reasonable size, can be wrong by a factor well in excess of 2.

Amino Acid Sequence↗

PubMed2005

The earliest modern mongoose (Carnivora, Herpestidae) from Africa (late Miocene of Chad).

We report on the earliest modern mongooses of Africa, from the late Miocene (ca. 7 Ma) of the hominid locality TM 266, Toros-Menalla, Chad. The material is based on fragmentary dentitions of three individuals. The main diagnostic feature of the Chadian species is the great development of the shear in the carnassials, which distinguishes the Chadian specimens from all extant herpestids except Herpestes and Galerella. In comparison with most extinct and extant Herpestes, the species from Toros-Menalla differs by a markedly smaller size and, depending on the species, relatively more elongated carnassials, more transversely elongated M1 and more reduced p4. On the basis of a great morphological similarity and the absence of significant differences, we assign our material to Galerella sanguinea; the Chadian finding therefore represents the earliest appearance of an extant species of Herpestidae. This record ties the first appearance of the genus to a minimum age of ca. 7 Ma, which is consistent with the estimated divergence date of 11.4 Ma known from the literature for the species of Galerella.

Africa↗

PubMed2003

Estimating changes in mutational mechanisms of evolution.

By considering three DNA sequences simultaneously there is sufficient information to recover a full Markov model with three transition matrices from the root to each of the sequences. It is necessary to have relatively long sequences because, for nucleotides, the full model requires 39 parameters that are estimated from 63 observable values. This triplet Markov method is evaluated for the protein coding genes of mammalian vertebrate mitochondrial genomes, and, in addition, version for two-state-characters (such as R/Y coding) is implemented. A key finding is that some changes in mutational mechanism differentially affect the mutation rate between pairs of nucleotides: there does not appear to be a universal change in "rate" of evolution. It remains to be explored whether detecting changes in certain nucleotide interchanges can be localized to a particular part of the DNA replication/repair system. In order to estimate divergence dates it may eventually be advantageous to use the nucleotide interchanges that show little rate change.

Animals↗