Evolutionary relationship ofHLA-DRB genes inferred from intron sequences

The major histocompatibility complex (Mhc) consists of class I and class II genes. In the humanMhc (HLA) class II genes, nineDRB loci have been identified. To elucidate the origin of these duplicated loci and allelic divergences at the most polymorphicDRBI locus, introns 4 and 5 as well as the 3′ untranslated region (altogether approximately 1,000 base pairs) of sevenHLA-DRB loci, threeHLA-DRBI alleles, and nine nonhuman primateDRB genes were examined. It is shown that there were two major diversification events inHLA-DRB genes, each involving gene duplications and allelic divergences. Approximately 50 million years (my) ago,DRBI ^*04 and an ancestor of theDRB1 ^*03 cluster (DRBI ^*03, DRBI^*15, andDRB3) diverged from each other andDRB5, DRB7, DRB8, and an ancestor of theDRB2 cluster (DRB2, DRB4, andDRB6) arose by gene duplication. Later, about 25 my ago,DRBI ^*15 diverged fromDRBI*03, andDRB3 was duplicated fromDRBI ^*03. Then, some 20 my ago, the lineage leading to theDRB2 cluster produced two new loci,DRB4 andDRB6. TheDRBI ^*03 andDRBI ^*04 allelic lineages are extraordinarily old and have persisted longer than some duplicated genes. The orthologous relationships ofDRB genes between human and Old World monkeys are apparent, but those between Catarrhini and New World monkeys are equivocal because of a rather rapid expansion and contraction of primateDRB genes by duplication and deletion. Correspondence to: Y. Satta     

Phylogenetic analysis of the perissodactylan family Tapiridae using mitochondrial cytochromec oxidase (COII) sequences

The four extant members of the family Tapiridae have a disjunct, relictual distribution, with three species being Neotropical (Tapirus bairdii, T. terrestris, andT. pinchaque) and one found in Southeast Asia (T. indicus). Little recent work on tapir systematics have appeared, and no molecular studies of this group have been published. A phylogenetic analysis was undertaken using sequences of the mitochondrial cytochromec oxidase subunit II gene (COII) from representatives of the four species of tapirs, as well as a representative outgroup,Equus caballus. Analyses of the COII sequences indicate a close relationship between the two South American species of tapirs,T. terrestris andT. pinchaque, and estimates of divergence dates using rates of COII evolution are compatible with migration of a single tapir lineage into South America following the emergence of the isthmus of Panama, about 3 million years bp. Various methods of analysis, including maximum parsimony, maximum likelihood, and neighbor-joining, provided poorer resolution of other tapir relationship. The COII data suggest that three distinct tapir mitochondrial lineages, a South American (represented byT. terrestris andT. pinchaque), a Central American (represented byT. bairdii), and an Asian (represented byT. indicus) diverged relatively rapidly, 20–30 million years bp. Another goal of this study was to calibrate the rate of COII evolution in a eutherian mammal group which has a good fossil record, such as perissodactyls, to estimate accurately the rate of COII evolution in a nonprimate mammalian group. The rate of COII evolution in equids and tapirs has been relatively constant and, using corrected distances, calibrated to be approximately 0.22% lineage/million years. This rate is three-to fourfold lower than that of hominoid primates.     

Molecular Phylogenetics of Gadidae and Related Gadiformes Based on Mitochondrial DNA Sequences

Mitochondrial DNA sequences of selected regions of the small subunit and large subunit ribosomal RNAs and cytochrome b genes were analyzed for 10 gadid species, representing 8 genera within Gadidae, and 10 species representing 5 other gadiform families. Phylogenetic analyses revealed that Gadiculus is the most basal gadid genus, and that Trisopterus and Micromesistius constitute a relatively basal clade. Lotidae was identified as the family most closely related to Gadidae. Estimation of divergence times indicated that the most ancient Gadidae split between Gadiculus and the remaining gadid genera occurred about 20 million years ago. The clade including the most recent species (Gadus, Boreogadus, Merlangius, Melanogrammus, and Pollachius) diverged from the Trisopterus/Micromesistius clade approximately 12 million years ago.     

Comparison of the nucleotide sequences of the meta-cleavage pathway genes of TOL plasmid pWW0 from Pseudomonas putida with other meta-cleavage genes suggests that both single and multiple nucleotide substitutions contribute to enzyme evolution

TOL plasmid pWW0 from Pseudomonas putida mt-2 encodes catabolic enzymes required for the oxidation of toluene and xylenes. The structural genes for these catabolic enzymes are clustered into two operons, the xylCMABN operon, which encodes a set of enzymes required for the transformation of toluene/xylenes to benzoate/toluates, and the xylXYZLTEGFJQKIH operon, which encodes a set of enzymes required for the transformation of benzoate/toluates to Krebs cycle intermediates. The latter operon can be divided physically and functionally into two parts, the xylXYZL cluster, which is involved in the transformation of benzoate/toluates to (methyl)catechols, and the xylTEGFJQKIH cluster, which is involved in the transformation of (methyl)catechols to Krebs cycle intermediates. Genes isofunctional to xylXYZL are present in Acinetobacter calcoaceticus, and constitute a benzoate-degradative pathway, while xylTEGFJQKIH homologous encoding enzymes of a methylphenol-degradative pathway and a naphthalene-degradative pathway are present on plasmid pVI150 from P. putida CF600, and on plasmid NAH7 from P. putida PpG7, respectively. Comparison of the nucleotide sequences of the xylXYZLTEGFJQKIH genes with other isofunctional genes suggested that the xylTEGFJQKIH genes on the TOL plasmid diverged from these homologues 20 to 50 million years ago, while the xylXYZL genes diverged from the A. calcoaceticus homologues 100 to 200 million years ago. In codons where amino acids are not conserved, the substitution rate in the third base was higher than that in synonymous codons. This result was interpreted as indicating that both single and multiple nucleotide substitutions contributed to the amino acid-substituting mutations, and hence to enzyme evolution. This observation seems to be general because mammalian globin genes exhibit the same tendency.     

Phylogenetic relationships within the New Zealand frog genus Leiopelma — immunological evidence

Abstract

Albumin evolution is examined within the anuran genus Leiopelma using the quantitative immunological technique of micro-complement fixation (MC'F). The albumins of L. archeyi and L. hamiltoni are relatively similar to each other, yet both differ greatly from the albumin of L. hochstetteri. Using albumin as a molecular clock, we estimate that L. hochstetteri diverged from the lineage leading to L. archeyi and L. hamiltoni during the Miocene, about 15 million years ago. The divergence of L. archeyi and L. hamiltoni appears to have been a Pliocene event (about 3 million years ago).     

Amino acid sequences of stomach and nonstomach lysozymes of ruminants

Summary Complete amino acid sequences are presented for lysozymesc from camel and goat stomachs and compared to sequences of other lysozymesc. Tree analysis suggests that the rate of amino acid replacement went up as soon as lysozyme was recruited for the stomach function in early ruminants. The two lysozymes from goat stomach are the products of a gene duplication that probably took place before the divergence of cow, goat, and deer about 25 million years ago. Partial sequences of three lysozymes from goat tears indicated that (a) the goat tear family of lysozymes may have diverged from the stomach lysozyme family by an ancient duplication and (b) later duplications are probably responsible for the multiple forms of tear and milk lysozymes in ruminants.     

Phylogeny and Evolutionary History of the Ground Squirrels (Rodentia: Marmotinae)

Although ground squirrels (Spermophilus) and prairie dogs (Cynomys) are among the most intensively studied groups of mammals with respect to their ecology and behavior, a well-resolved phylogeny has not been available to provide a framework for comparative and historical analyses. We used complete mitochondrial cytochrome b sequences to construct a phylogeny that includes all 43 currently recognized species in the two genera, as well as representatives of two closely related genera (Marmota and Ammospermophilus). In addition, divergence times for ground squirrel lineages were estimated using Bayesian techniques that do not assume a molecular clock. All methods of phylogenetic analysis recovered the same major clades, and showed the genus Spermophilus to be paraphyletic with respect to both Marmota and Cynomys. Not only is the phylogeny at odds with previous hypotheses of ground squirrel relationships, but it suggests that convergence in morphology has been a common theme in ground squirrel evolution. A well-supported basal clade, including Ammospermophilus and two species in the subgenus Otospermophilus, diverged from all other ground squirrels an estimated 17.5 million years ago. Between 10 and 14 million years ago, a relatively rapid diversification gave rise to lineages leading to marmots and to several distinct groups of ground squirrels. The Eurasian ground squirrels diverged from their North American relatives during this period, far earlier than previously hypothesized. This period of diversification corresponded to warming climate and spread of grasslands in western North America and Eurasia. Close geographic proximity of related forms suggests that most species evolved in or near their current ranges.     

Speciation in the greater galagos (Prosimii: Galaginae): review and synthesis*

A marked morphological and genetical discontinuity among the greater galagos points to the existence of two genetical species within the taxon, Galago crassicaudatus E. Geofl'roy 1812. This contribution investigates the conditions surrounding this speciation event, and places it within a phylogenetic context. Information pertaining to body size, litter size, sexual dimorphism, locomotor mode and karyotypic structure is assessed. It is hypothesized that G. crassicaudatus diverged from its more gracile sibling, G. garnettii, approximately 2 million years ago, in respotise lo the increasing aridification of Africa that accompanied the Northern Hemisphere Pleistocene glaciations.     

cDNA and deduced amino acid sequences of cytochrome c fromChlamydomonas reinhardtii: Unexpected functional and phylogenetic implications

Summary We have isolated complementary DNA (cDNA) clones for apocytochrome c from the green algaChlamydomonas reinhardtii and shown that they are encoded by a single nuclear gene termedcyc.Cyc mRNA levels are found to depend primarily on the presence of acetate as a reduced carbon source in the culture medium. The deduced amino acid sequence shows that, apart from the probable removal of the initiating methionine,C. reinhardtii apocytochrome c is syntheszed in its mature form. Its structure is generally similar to that of cytochromes c from higher plants. Several punctual deviations from the general pattern of cytochrome c sequences that is found in other organisms have interesting structural and functional implications. These include, in particular, valines 19 and 39, asparagine 78, and alanine 83. A phylogenetic tree was constructed by the matrix method from cytochrome c data for a representative range of species. The results suggest thatC. reinhardtii diverged from higher plants approximately 700–750 million years ago; they also are not easy to reconcile with the current attribution ofChlamydomonas reinhardtii andEnteromorpha intestinalis to a unique phylum, because these two species probably diverged from one another at about the same time as they diverged from the line leading to higher plants.     

Identification of two Drosophila TGF-β family members in the grasshopper Schistocerca americana

Intercellular signaling molecules of the transforming growth factor- (TGF-) superfamily are required for pattern formation in many multicellular organisms. The decapentaplegic (dpp) gene of Drosophila melanogaster has several developmental roles. To improve our understanding of the evolutionary diversification of this large family we identified dpp in the grasshopper Schistocerca americana. S. americana diverged from D. melanogaster approximately 350 million years ago, utilizes a distinct developmental program, and has a 60-fold-larger genome than D. melanogaster. Our analyses indicate a single dpp locus in D. melanogaster and S. americana, suggesting that dpp copy number does not correlate with increasing genome size. Another TGF- superfamily member, the D. melanogaster gene 60A, is also present in only one copy in each species. Comparison of homologous sequences from D. melanogaster, S. americana, and H. sapiens, representing roughly 900 million years of evolutionary distance, reveals significant constraint on sequence divergence for both dpp and 60A. In the signaling portion of the dpp protein, the amino acid identity between these species exceeds 74%. Our results for the TGF- superfamily are consistent with current hypotheses describing gene duplication and diversification as a frequent response to high levels of selective pressure on individual family members.     

The evolution of skeletal muscle performance: gene duplication and divergence of human sarcomeric α‐actinins

In humans, there are two skeletal muscle α‐actinins, encoded by ACTN2 and ACTN3, and the ACTN3 genotype is associated with human athletic performance. Remarkably, approximately 1 billion people worldwide are deficient in α‐actinin‐3 due to the common ACTN3 R577X polymorphism. The α‐actinins are an ancient family of actin‐binding proteins with structural, signalling and metabolic functions. The skeletal muscle α‐actinins diverged ～250–300 million years ago, and ACTN3 has since developed restricted expression in fast muscle fibres. Despite ACTN2 and ACTN3 retaining considerable sequence similarity, it is likely that following duplication there was a divergence in function explaining why α‐actinin‐2 cannot completely compensate for the absence of α‐actinin‐3. This paper focuses on the role of skeletal muscle α‐actinins, and how possible changes in functions between these duplicates fit in the context of gene duplication paradigms.     

Phosphorylation network rewiring by gene duplication

Elucidating how complex regulatory networks have assembled during evolution requires a detailed understanding of the evolutionary dynamics that follow gene duplication events, including changes in post‐translational modifications. We compared the phosphorylation profiles of paralogous proteins in the budding yeast Saccharomyces cerevisiae to that of a species that diverged from the budding yeast before the duplication of those genes. We found that 100 million years of post‐duplication divergence are sufficient for the majority of phosphorylation sites to be lost or gained in one paralog or the other, with a strong bias toward losses. However, some losses may be partly compensated for by the evolution of other phosphosites, as paralogous proteins tend to preserve similar numbers of phosphosites over time. We also found that up to 50% of kinase–substrate relationships may have been rewired during this period. Our results suggest that after gene duplication, proteins tend to subfunctionalize at the level of post‐translational regulation and that even when phosphosites are preserved, there is a turnover of the kinases that phosphorylate them.     

Evolutionary History and Mode of the <Emphasis Type="Italic">amylase</Emphasis> Multigene Family in <Emphasis Type="Italic">Drosophila</Emphasis>

Previous studies indicate that the tandemly repeated members of the amylase (Amy) gene family evolved in a concerted manner in the melanogaster subgroup and in some other species. In this paper, we analyzed all of the 49 active and complete Amy gene sequences in Drosophila, mostly from subgenus Sophophora. Phylogenetic analysis indicated that the two types of diverged Amy genes in the Drosophila montium subgroup and Drosophila ananassae, which are located in distant chromosomal regions from each other, originated independently in different evolutionary lineages of the melanogaster group after the split of the obscura and melanogaster groups. One of the two clusters was lost after duplication in the melanogaster subgroup. Given the time, 24.9 mya, of divergence between the obscura and the melanogaster groups (Russo et al. 1995), the two duplication events were estimated to occur at about 13.96 ± 1.93 and 12.38 ± 1.76 mya in the montium subgroup and D. ananassae, respectively. An accelerated rate of amino acid changes was not observed in either lineage after these gene duplications. However, the G+C contents at the third codon positions (GC3) decreased significantly along one of the two Amy clusters both in the montium subgroup and in D. ananassae right after gene duplication. Furthermore, one of the two types of the Amy genes with a lower GC3 content has lost a specific regulatory element within the montium subgroup species and D. ananassae. While the tandemly repeated members evolved in a concerted manner, the two types of diverged Amy genes in Drosophila experienced frequent gene duplication, gene loss, and divergent evolution following the model of a birth-and-death process.     

Of mice and men: Fossil-based divergence dates and molecular “clocks”

The magnitude of immunological differences between species has been used to estimate the time of divergence of lineages, especially among primates. Calibration of “clocks” based on immunological differences has relied heavily on data from Pakistan suggest that the lineages leading to Mus and Rattus diverged between 14 and 8 million years ago rather than 30 or more million years ago as suggested by techniques invoking constant rates of molecular evolution. Molecular analyses of pairs of mammal species which appear well documented paleontologically should be undertaken in order to expand our understanding of the tempo and mode of molecular evolution.     

Molecular Phylogenetic Analysis of Petunia Juss. (Solanaceae)

Representatives from 11 Petunia Jussieu species in south and southeast Brazil were compared with two Calibrachoa La Llave & Lex., one Bouchetia Dunal, and two Nierembergia Ruiz & Pav. taxa in relation to DNA molecular variability. A total of 4532 base pairs related to one nuclear, five plastidial and one mitochondrial systems was investigated. Petunia and Calibrachoa, although separated among themselves, clearly differentiate from the two other genera. Despite the fact that the Petunia species do not show marked molecular differences, they can be separated in two complexes, in good agreement with altitude data. Petunia + Calibrachoa should have diverged from other clades at about 25 million years before present.     

Recent duplication and positive selection of the <Emphasis Type="Italic">GAGE</Emphasis> gene family

We report that the GAGE gene family of human Cancer/testis antigen (CTA) genes is likely to be in an early stage of its evolution. Members of this gene family are tandemly arranged on the X chromosome only in human, chimpanzee and macaque genomes and share a very high similarity. Phylogenetic trees show that the GAGE gene family began to duplicate after the split of human and chimpanzee. The estimated ages of the duplication events range from 4 million years ago to the present. The Ka/Ks values between the duplicates are significantly greater than 1, indicating that the mutation rate is higher in coding regions than non-coding regions of the genes, which suggests that the GAGE gene family is under positive selection. These findings indicate that the GAGE gene family may be a newly formed gene family undergoing rapid functional evolution. Yang Liu and Qiyun Zhu contributed equally to this work.     

Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata

How do populations of highly mobile species inhabiting open environments become reproductively isolated and evolve into new species? We test the hypothesis that elevated ocean‐surface temperatures can facilitate allopatry among pelagic populations and thus promote speciation. Oceanographic modelling has shown that increasing surface temperatures cause localization and reduction of upwelling, leading to fragmentation of feeding areas critical to pelagic species. We test our hypothesis by genetic analyses of populations of two closely related baleen whales, the Antarctic minke whale (Balaenoptera bonaerensis) and common minke whale (Balaenoptera acutorostrata) whose current distributions and migration patterns extent are largely determined by areas of consistent upwelling with high primary production. Phylogeographic and population genetic analyses of mitochondrial DNA control‐region nucleotide sequences collected from 467 whales sampled in four different ocean basins were employed to infer the evolutionary relationship among populations of B. acutorostrata by rooting an intraspecific phylogeny with a population of B. bonaerensis. Our findings suggest that the two species diverged in the Southern Hemisphere less than 5 million years ago (Ma). This estimate places the speciation event during a period of extended global warming in the Pliocene. We propose that elevated ocean temperatures in the period facilitated allopatric speciation by disrupting the continuous belt of upwelling maintained by the Antarctic Circumpolar Current. Our analyses revealed that the current populations of B. acutorostrata likely diverged after the Pliocene some 1.5 Ma when global temperatures had decreased and presumably coinciding with the re‐establishment of the polar–equatorial temperature gradient that ultimately drives upwelling. In most population samples, we detected genetic signatures of exponential population expansions, consistent with the notion of increasing carrying capacity after the Pliocene. Our hypothesis that prolonged periods of global warming facilitate speciation in pelagic marine species that depend on upwelling should be tested by comparative analyses in other pelagic species.     

Intergeneric Relationships Among Macropodoidea (Metatheria: Diprotodontia) and The Chronicle of Kangaroo Evolution

The superfamily of kangaroos (Macropodoidea) is comprised of the subfamilies Propleopinae, Hypsiprymnodontinae, Paleopotoroinae, Potoroinae, Bulungamayinae, Balbarinae, Macropodinae, and Sthenurinae. Of these, Hypsiprymnodontinae, Potoroinae, and Macropodinae are extant. Competing phylogenetic hypotheses unite potoroines with either hypsiprymnodontines or macropodines, with most recent workers following a classificatory scheme that recognizes Hypsiprymnodontidae (hypsiprymnodontines) and Macropodidae (macropodines + potoroines). To address phylogenetic relationships among living macropodoids, we analyzed sequences from three mitochondrial genes (12S rRNA, tRNA valine, 16S rRNA) and one nuclear gene (protamine P1). MtDNA and protamine P1 both support a basal split of Hypsiprymnodon from other macropodoids rather than an association of Hypsiprymnodon with potoroines. This suggests that bipedal hopping and a complex stomach evolved once among macropodids. Monophyly of the Macropodinae is supported. Among macropodines, there is support for a Dorcopsis-Dorcopsulus association. Potoroine monophyly is less clear, although among potoroines there is support for an association of Bettongia and Aepyprymnus. Divergence times were estimated using 12S rRNA, tRNA-valine, and 16S rRNA transversions and suggest that kangaroos separated from a possum-like ancestor approximately 38–44 million years ago. Hypsiprymnodon diverged from other macropodoids approximately 34 to 38 million years ago. In agreement with the fossil record, the diversification of potoroines predates the diversification of macropodines. The latter have radiated in association with the development of a more arid climate and emergent grasslands over the Australian continent.