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PubMed2026

Discovery and evolution of endogenous retroviruses in the genome of crab-eating macaque (Macaca fascicularis).

Endogenous retroviruses (ERVs) are a dynamic and biologically significant component of vertebrate genomes, with integration events spanning deep evolutionary time. The crab-eating macaque (Macaca fascicularis) is an important non-human primate model for biomedical research because of its close phylogenetic relationship to humans and its conservation status as an endangered species. However, the ERV complement of its genome has not been systematically characterized. Using the current highest-quality chromosome-level genome assembly for this species, we performed a genome-wide, homology-based survey of relatively intact ERV proviruses in M. fascicularis. We identified 106 proviral loci distributed across all chromosomes. Phylogenetic reconstruction based on conserved reverse transcriptase domains classified these elements into β-, γ-, and unclassified lineages, with β- and γ-retroviral lineages predominating. LTR divergence-based dating indicated that these proviruses represent multiple waves of historical retroviral activity and span a broad range of integration ages. This curated dataset provides a high-confidence reference set for investigating the evolutionary history and genomic impact of preserved ERV proviruses in an endangered primate model; however, it does not include degraded ERV fragments or solo LTRs.

Animals↗
PubMed2026

Parting ways: Pan-Homo divergence revisited.

The timing of divergence between hominins and the bonobo-chimpanzee clade has been at the core of palaeoanthropological debate for over a century. The earliest molecular studies indicated divergence times ranging from 5 Ma to as recently as 1.3 Ma. This study critically reviews the trends of time estimates published between 1967 and 2023, and analyses how these are supported or rejected by the current molecular and fossil records. We compiled 202 divergence estimates and defined three distinct thresholds based on fossil evidence at 4.4 Ma (Australopithecus anamensis and Ardipithecus ramidus), 6.2 Ma (Orrorin tugenensis and Ardipithecus kadabba), and 7.2 Ma (Sahelanthropus tchadensis). We then used these thresholds to filter out molecular estimates that are too young to fit the fossil record. Overall, the data suggests a divergence event within the late Miocene, with each threshold pushing it further back, 8.63-6.38, 10.33-7.81, and 10.95-8.81 Ma, respectively. We use a quadratic regression to demonstrate that estimates have been slowly shifting from ~ 6 Ma to ~ 8.5 Ma over the past 56 years. A Bayesian meta-analysis of genomic estimates filtered by our most consensual threshold (i.e., assuming Australopithecus belongs to Hominini) indicates that the split must have occurred early in the late Miocene, most likely before 7 Ma (~ 99.5% posterior probability) with a pooled effect of 8.69-7.28 Ma. We conclude that, despite an initial bias towards younger estimates, the molecular timing for the last common ancestor (LCA) of Pan-Homo has been progressively approaching the intervals suggested by the current fossil record.

Animals↗
PubMed1990

Drosophila melanogaster troponin-T mutations engender three distinct syndromes of myofibrillar abnormalities.

In vertebrates troponin complexes interact co-operatively with tropomyosin dimers to modulate skeletal muscle contraction. In order further to investigate troponin assembly and function in vivo, we are developing molecular genetic approaches. Here we report characterization of the gene that encodes Drosophila tropinin-T and analyses of muscle defects engendered by several mutant alleles. We found that the Drosophila troponin-T locus specifies at least three proteins having sequences similar to vertebrate troponin-T. All are significantly larger than any avian or mammalian isoforms, however, due to a highly acidic carboxy-terminal extension. Comparisons of the chromosomal arrangements of vertebrate and Drosophila troponin-T genes revealed that the location of one intron-exon boundary is conserved. This observation and the similarity of vertebrate and Drosophila troponin-T primary sequences suggest that the respective proteins are homologous, and that troponin-T pre-dates the divergence of vertebrate and invertebrate organisms. In situ hybridization of the Drosophila troponin-T gene to polytene chromosomes demonstrated that it resides within subdivision 12A of the X chromosome, precisely where upheld and indented thorax flight muscle mutations have been mapped previously. We determined the nucleotide sequences of troponin-T genes in five extant mutants. All have deleterious alterations, directly establishing that upheld and indented thorax muscle abnormalities are due to defective troponin-T. Two of the alleles, upheld2 and upheld3, apparently disrupt RNA splicing and eliminate most or all troponin-T from flight and jump muscles, while the remaining three alleles change the identities of single amino acids of troponin-T. Electron microscopy of mutant muscles revealed that the two null alleles eliminate thin filaments, except where they are bound by electron-dense material presumed to be Z-disc proteins. Two of the point mutations, upheld101 and indented thorax3, do not perturb assembly of myofibrils, but cause their degeneration within days after muscles begin to be utilized. The final mutation, upheldwhu, reduces the diameter of the myofibril lattice by approximately one-half. We propose hypotheses to explain how each troponin-T mutation engenders the observed myofibrillar defects.

Alleles↗
PubMed2005

Coalescent models reveal the relative roles of ancestral polymorphism, vicariance, and dispersal in shaping phylogeographical structure of an African montane forest robin.

Although many studies have documented the effect of glaciation on the evolutionary history of Northern Hemisphere flora and fauna, this study is the first to investigate how the indirect aridification of Africa caused by global cooling in response to glacial cycles at higher latitudes has influenced the evolutionary history of an African montane bird. Mitochondrial DNA sequences from the NADH 3 gene were collected from 283 individual Starred Robins (Pogonocichla stellata, Muscicapoidea). At least two major vicariant events, one that separated the Albertine Rift from all but the Kenyan Highlands around 1.3-1.2 Myrs BP, and another that separated the Kenyan Highlands from the northern Eastern Arc, and the northern Eastern Arc from the south-central Eastern Arc between 0.9 and 0.8 Myrs BP appear to underlie much of the observed genetic diversity and structure within Starred Robin populations. These dates of divergence suggest a lack of recurrent gene flow; although the Albertine Rift and south-central Eastern Arc share haplotypes, based on coalescent analyses this can confidently be accounted for by ancestral polymorphism as opposed to recurrent gene flow. Taken collectively, strong evidence exists for recognition of four major ancestral populations: (1) Kenyan Highlands (subspecies keniensis), (2) Albertine Rift (ruwenzori), (3) northern Eastern Arc (helleri), and (4) south-central Eastern Arc, Ufipa and the Malawi Rift (orientalis). The estimated divergence times cluster remarkably around one of the three estimated peaks of aridification in Africa during the Plio-Pleistocene centred on 1 Myrs BP. Further, time to most recent common ancestor (TMRCA) estimates (1.7-1.6 Myrs BP) of gene divergence between the Albertine Rift and the other montane highlands corresponds closely with a second estimated peak of aridification at about 1.7 Myrs BP. Collectively, these results suggest that aridification of Africa in response to glaciation at higher latitudes during the Pleistocene has had a profound influence on montane speciation in east and central Africa.

Africa↗
PubMed2006

Phylogeography and demographic history of the deep-sea fish Aphanopus carbo (Lowe, 1839) in the NE Atlantic: Vicariance followed by secondary contact or speciation?

Comparative phylogeography for the commercially valuable deep-sea fish Aphanopus carbo from a large area of the NE Atlantic revealed remarkable patterns of concordance using two mtDNA markers. Two strongly supported phylogroups were identified from complete sequences of the control region (731-733 bp) and partial sequences of cytochrome b (414 bp) In one of these groups, all sequences from the Mid-Atlantic Ridge (Faraday seamount), mainland Portugal and Madeira were clustered together. The other group constituted all the sequences from the southern coast of Pico island (Azores, central group). The remaining sampling localities had sequences represented in both phylogroups. Although the two clades were strongly differentiated (Phi(ST) = 0.8281 for the CR and Phi(ST) = 0.9083 for the cytb) no evidence for any geographical pattern in this structure, was found. Historical demography of the mitochondrial control region was analysed to clarify the phylogenetic signals embedded in each phylogroup. Mismatch distributions for both clades suggested that both phylogroups were in agreement with sudden expansion models, and both with similar time estimates of expansion (tau = 4.30 and tau = 3.45 for phylogroup one and two, respectively). A molecular clock based on cytb sequences was enforced and dating of divergence for the two phylogroup was 412.5 KY, a time that coincides with geological events that might have caused a split in the original population of black scabbardfish. Once climatic conditions and sea level were restored, the two separate populations came into contact again, leaving traces of the historical events in the non-recombinant mtDNA genes. An alternative hypothesis suggested is that two species of scabbardfish are present. The outcome from the comparison of the same mtDNA regions of the closely related Aphanopus intermedius from Angola clustered with the ones from phylogroup two (from the southern coast of Pico island, Azores). Therefore, these two species may have overlapping distribution ranges and are found sympatrically in the Azores.

Animals↗
PubMed2006

Evolution of host specialization in the Adelgidae (Insecta: Hemiptera) inferred from molecular phylogenetics.

The Adelgidae form a small group of insects in the Aphidoidea. They are cyclically parthenogenetic with host alternating, multiple-generation complex life cycles and are restricted to certain host genera in the Pinaceae. Species that host alternate always have Picea as the primary host where sexual reproduction and gall formation occur, and another genus in the Pinaceae as the secondary host where a series of parthenogenetic generations are produced. Other species that do not host alternate complete their entire life cycle on one host and only reproduce parthenogenetically. We studied relationships within Adelgidae using DNA sequences from the mitochondrial COI, COII, and cytb genes, and the nuclear EF1alpha gene. Analysis of the combined data resulted in a well-resolved phylogeny in which the major adelgid clades correspond neatly to their association with secondary host genera. Specialization on each secondary host genus occurred only once and was followed by diversification on the host genus. Molecular dating of divergence times in the Adelgidae suggest that diversification among host genera occurred in the Late Cretaceous and Early Tertiary when the Pinaceae genera were diverging. It is not clear, however, whether the Adelgidae and Pinaceae co-diversified because the relationships among the Pinaceae genera are not fully resolved. We discuss implications for adelgid taxonomy, life cycle evolution, and evolution of the interaction between adelgids and their host plants.

Animals↗
PubMed1982

The relationships of Sivapithecus and Ramapithecus and the evolution of the orang-utan.

We review here the molecular data that bear on and provide a framework for interpreting hominoid relationships. Man is shown to be most closely related to chimpanzees and gorillas among extant hominoids, with the orang-utan more distantly related to them and the gibbons more distantly still. A fossil ape, Sivapithecus meteai, shares several characters with the orang-utan and is thus probably related to it. S. meteai is part of the Middle Miocene Sivapithecus-Ramapithecus species complex, and if this group forms a valid clade then Ramapithecus must also be considered as being more closely related to the orang-utan than to man. The date of divergence of the orang-utan from the African apes and man is suggested by fossil and molecular evidence to be 10 +/- 3 Myr ago.

Animals↗
PubMed1988

The Drosophila gene knirps-related is a member of the steroid-receptor gene superfamily.

Molecular cloning has demonstrated that the receptors for steroid, retinoid and thyroid hormones are part of a large superfamily of nuclear regulatory proteins. In vertebrates these molecules regulate diverse biological processes such as pattern formation, cellular differentiation and homeostasis. The universal necessity for embryonic and adult cells to respond to their external environment might mean that members of this family pre-date the divergence of vertebrates and invertebrates. We have screened a Drosophila genomic library for steroid receptor homologues using a human retinoic acid receptor complementary DNA as a hybridization probe. Several clones were recovered, one of which mapped to chromosomal position 77E1-2, the cytological location of the gap segmentation gene knirps. Sequence analysis of a cDNA clone representing the human retinoic acid receptor homologue showed similarity of the predicted protein to the vertebrate steroid receptors, as well as to the predicted knirps gene product. In situ hybridization of a cDNA probe to wild-type embryos revealed a uniform distribution of transcripts that were apparently maternally derived. Zygotic transcript accumulation begins in a broad anteroventral domain before the cellular blastoderm stage. At the cellular blastoderm stage two additional circumferential bands of transcript appear.

Amino Acid Sequence↗
PubMed2004

Mitochondrial simple sequence repeats and 12S-rRNA gene reveal two distinct lineages of Crocidura russula (Mammalia, Soricidae).

A short segment (135 bp) of the control region and a partial sequence (394 bp) of the 12S-rRNA gene in the mitochondrial DNA of Crocidura russula were analyzed in order to test a previous hypothesis regarding the presence of a gene flow disruption in northern Africa. This breakpoint would have separated northeast-African C. russula populations from the European (plus the northwest-African) populations. The analysis was carried out on specimens from Tunisia (C. r. cf agilis), Sardinia (C. r. ichnusae), and Pantelleria (C. r. cossyrensis), and on C. r. russula from Spain and Belgium. Two C. russula lineages were identified; they both shared R2 tandem repeated motifs of the same length (12 bp), but not the same primary structure. These simple sequence repeats were present in 12-23 copies in the right domain of the control region. Within the northeast-African populations, a polymorphism of repeat variants, not yet found in Europe, was recorded. A neighbor-join tree, which was built by sequences of the conserved 12S-rRNA gene, separated the two sister groups; it permitted us to date a divergence time of 0.5 Myr. Our data discriminated two different mitochondrial lineages in accordance with the previous morphological and karyological data. Ecoclimatic barriers formed during the Middle Pleistocene broke the range of ancestral species in the Eastern Algeria (Kabile Mountains), leading to two genetically separate and modern lineages. The northeast-African lineage can today be located in Tunisia, Pantelleria, and Sardinia. The northwest-African lineage (Morocco and West Algeria), reaching Spain by anthropogenic introduction, spread over north Europe in modern times. The Palaearctic C. russula species is monophyletic, but a taxonomical revision (ie, to provide a full species rank for the northeast taxa and to put in synonymy some insular taxa) is required.

Africa, Northern↗
PubMed1975

Studies on monotreme proteins. VI. Amino acid sequence of the beta-chain of haemoglobin from the platypus, Ornithorhynchus anatinus.

The amino acid sequence of the 146 residues of the beta-chain of the major haemoglobin from the platypus has been determined. The soluble peptides derived from the chain by tryptic digestion were isolated by paper ionophoresis and chromatography. The amino acid sequences were determined by the dansyl-Edman procedure or by further digestion with other enzymes. The tryptic peptides were aligned by homology with other beta-globins. There were 14 changes in sequence compared with echidna beta-chain. The number of changes in sequence compared with human beta-chain is 34 which is less than the 39 changes between human and platypus alpha-chains. Generally there are more changes between beta-chains; there are only three other examples reported where there are more changes between alpha-chains than beta-chains, these are of echidna, rabbit and dog globins. By comparison with the 'contact sites' in horse haemoglobin there is one change in beta-haem contacts, three changes in beta1-alpha1 contacts and no changes in beta2-alpha1 contacts. The date of divergence of the monotremes from the other mammals was estimated at 132 +/- 33 million years, based on the number of amino acid differences between species and allowing for multiple mutations during the evolutionary period. This estimate differs widely from the estimate given by similar treatment of the alpha-chain sequences and the significance of this discrepancy to the validity of the method is discussed.

Amino Acid Sequence↗
PubMed1997

Operons and SL2 trans-splicing exist in nematodes outside the genus Caenorhabditis.

The genomes of most eukaryotes are composed of genes arranged on the chromosomes without regard to function, with each gene transcribed from a promoter at its 5' end. However, the genome of the free-living nematode Caenorhabditis elegans contains numerous polycistronic clusters similar to bacterial operons in which the genes are transcribed sequentially from a single promoter at the 5' end of the cluster. The resulting polycistronic pre-mRNAs are processed into monocistronic mRNAs by conventional 3' end formation, cleavage, and polyadenylation, accompanied by trans-splicing with a specialized spliced leader (SL), SL2. To determine whether this mode of gene organization and expression, apparently unique among the animals, occurs in other species, we have investigated genes in a distantly related free-living rhabditid nematode in the genus Dolichorhabditis (strain CEW1). We have identified both SL1 and SL2 RNAs in this species. In addition, we have sequenced a Dolichorhabditis genomic region containing a gene cluster with all of the characteristics of the C. elegans operons. We show that the downstream gene is trans-spliced to SL2. We also present evidence that suggests that these two genes are also clustered in the C. elegans and Caenorhabditis briggsae genomes. Thus, it appears that the arrangement of genes in operons pre-dates the divergence of the genus Caenorhabditis from the other genera in the family Rhabditidae, and may be more widespread than is currently appreciated.

Animals↗
PubMed1997

Evolution of the primate lineage leading to modern humans: phylogenetic and demographic inferences from DNA sequences.

To date major divergences that occurred in the primate lineage leading to modern humans and to infer a demographic parameter (effective population size) of the ancestral lineage that existed at each divergence, a maximum likelihood method was applied to autosomal DNA sequence data currently available for pairs of orthologous genes between the human and each of the chimpanzee, gorilla, Old World monkey (OWM), and New World monkey (NWM). A statistical test is carried out to support the assumption that silent substitutions have accumulated in a clock-like fashion over loci between primate taxa or even among sites within a locus. It is shown that the human ancestral lineage became distinct from the NWM 57.5 million years (Myr) ago, the OWM 31 Myr ago, the gorilla 8.0 Myr ago, and the chimpanzee 4.5 Myr ago, and that the effective population size at these divergences was generally much greater than that of modern humans. It is argued that the human ancestral lineage branched off from the NWM and OWM earlier than once thought and that significant demographic changes might have occurred at different evolutionary stages, particularly at the hominid stage.

Animals↗
PubMed1999

DNA sequence of the mitochondrial hypervariable region II from the neandertal type specimen.

The DNA sequence of the second hypervariable region of the mitochondrial control region of the Neandertal type specimen, found in 1856 in central Europe, has been determined from 92 clones derived from eight overlapping amplifications performed from four independent extracts. When the reconstructed sequence is analyzed together with the previously determined DNA sequence from the first hypervariable region, the Neandertal mtDNA is found to fall outside a phylogenetic tree relating the mtDNAs of contemporary humans. The date of divergence between the mtDNAs of the Neandertal and contemporary humans is estimated to 465,000 years before the present, with confidence limits of 317,000 and 741,000 years. Taken together, the results support the concept that the Neandertal mtDNA evolved separately from that of modern humans for a substantial amount of time and lends no support to the idea that they contributed mtDNA to contemporary modern humans.

Amino Acid Sequence↗
PubMed2005

An empirical examination of the utility of codon-substitution models in phylogeny reconstruction.

Models of codon substitution have been commonly used to compare protein-coding DNA sequences and are particularly effective in detecting signals of natural selection acting on the protein. Their utility in reconstructing molecular phylogenies and in dating species divergences has not been explored. Codon models naturally accommodate synonymous and nonsynonymous substitutions, which occur at very different rates and may be informative for recent and ancient divergences, respectively. Thus codon models may be expected to make an efficient use of phylogenetic information in protein-coding DNA sequences. Here we applied codon models to 106 protein-coding genes from eight yeast species to reconstruct phylogenies using the maximum likelihood method, in comparison with nucleotide- and amino acid-based analyses. The results appeared to confirm that expectation. Nucleotide-based analysis, under simplistic substitution models, were efficient in recovering recent divergences whereas amino acid-based analysis performed better at recovering deep divergences. Codon models appeared to combine the advantages of amino acid and nucleotide data and had good performance at recovering both recent and deep divergences. Estimation of relative species divergence times using amino acid and codon models suggested that translation of gene sequences into proteins led to information loss of from 30% for deep nodes to 66% for recent nodes. Although computational burden makes codon models unfeasible for tree search in large data sets, we suggest that they may be useful for comparing candidate trees. Nucleotide models that accommodate the differences in evolutionary dynamics at the three codon positions also performed well, at much less computational cost. We discuss the relationship between a model's fit to data and its utility in phylogeny reconstruction and caution against use of overly complex substitution models.

Classification↗
PubMed2006

Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomes.

The settlement of the many island groups of Remote Oceania occurred relatively late in prehistory, beginning approximately 3,000 years ago when people sailed eastwards into the Pacific from Near Oceania, where evidence of human settlement dates from as early as 40,000 years ago. Archeological and linguistic analyses have suggested the settlers of Remote Oceania had ancestry in Taiwan, as descendants of a proposed Neolithic expansion that began approximately 5,500 years ago. Other researchers have suggested that the settlers were descendants of peoples from Island Southeast Asia or the existing inhabitants of Near Oceania alone. To explore patterns of maternal descent in Oceania, we have assembled and analyzed a data set of 137 mitochondrial DNA (mtDNA) genomes from Oceania, Australia, Island Southeast Asia, and Taiwan that includes 19 sequences generated for this project. Using the MinMax Squeeze Approach (MMS), we report the consensus network of 165 most parsimonious trees for the Oceanic data set, increasing by many orders of magnitude the numbers of trees for which a provable minimal solution has been found. The new mtDNA sequences highlight the limitations of partial sequencing for assigning sequences to haplogroups and dating recent divergence events. The provably optimal trees found for the entire mtDNA sequences using the MMS method provide a reliable and robust framework for the interpretation of evolutionary relationships and confirm that the female settlers of Remote Oceania descended from both the existing inhabitants of Near Oceania and more recent migrants into the region.

DNA, Mitochondrial↗
PubMed2002

Molecular clocks in reptiles: life history influences rate of molecular evolution.

Life history has been implicated as a determinant of variation in rate of molecular evolution amongst vertebrate species because of a negative correlation between body size and substitution rate for many molecular data sets. Both the generality and the cause of the negative body size trend have been debated, and the validity of key studies has been questioned (particularly concerning the failure to account for phylogenetic bias). In this study, a comparative method has been used to test for an association between a range of life-history variables-such as body size, age at maturity, and clutch size-and DNA substitution rate for three genes (NADH4, cytochrome b, and c-mos). A negative relationship between body size and rate of molecular evolution was found for phylogenetically independent pairs of reptile species spanning turtles, lizards, snakes, crocodile, and tuatara. Although this study was limited by the number of comparisons for which both sequence and life-history data were available, the results suggest that a negative body size trend in rate of molecular evolution may be a general feature of reptile molecular evolution, consistent with similar studies of mammals and birds. This observation has important implications for uncovering the mechanisms of molecular evolution and warns against assuming that related lineages will share the same substitution rate (a local molecular clock) in order to date evolutionary divergences from DNA sequences.

Aging↗
PubMed2006

Evolutionary processes during the formation of the plant-specific Dof transcription factor family.

We found 19 putative genes for plant-specific Dof transcription factors in the moss Physcomitrella patens and one Dof gene in the green alga Chlamydomonas reinhardtii, but no identifiable Dof gene in the red alga Cyanidioschyzon merolae and the diatom Thalassiosira pseudonana, suggesting that the origin of the Dof transcription factors pre-dates the divergence of the green algae and the ancestors of terrestrial plants. The phylogenetic analyses contended that the Dof family in angiosperms formed through a series of evolutionary processes, including intensive duplications of a specific ancestral gene after the divergence of the moss and the angiosperm lineages.

Algal Proteins↗