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Common Ancestor (common + ancestor)
Kinds of Common Ancestor Selected AbstractsTIME TO THE MOST RECENT COMMON ANCESTOR AND DIVERGENCE TIMES OF POPULATIONS OF COMMON CHAFFINCHES (FRINGILLA COELEBS) IN EUROPE AND NORTH AFRICA: INSIGHTS INTO PLEISTOCENE REFUGIA AND CURRENT LEVELS OF MIGRATIONEVOLUTION, Issue 1 2002Cortland K. Griswold Abstract We analyzed sequences from a 275-bp hypervariable region in the 5, end of the mitochondrial DNA control region in 190 common chaffinches (Fringilla coelebs) from 19 populations in Europe and North Africa, including new samples from Greece and Morocco. Coalescent techniques were applied to estimate the time to the most recent common ancestor (TMRCA) and divergence times of these populations. The first objective of this study was to infer the locations of refugia where chaffinches survived the last glacial episode, and this was achieved by estimating the TMRCA of populations in regions surrounding the Mediterranean that were unglaciated in the late Pleistocene. Although extant populations in Iberia, Corsica, Greece, and North Africa harbor haplotypes that are basal in a phylogenetic tree, this information alone cannot be used to infer that these localities served as refugia, because it is impossible to infer the ages of populations and their divergence times without also considering the population genetic processes of mutation, migration, and drift. Provided we assume the TMRCAs of populations are a reasonable estimate of a population's age, coalescent-based methods place resident populations in Iberia, Corsica, Greece, and North Africa during the time of the last glacial maximum, suggesting these regions served as refugia for the common chaffinch. The second objective was to determine when populations began diverging from each other and to use this as a baseline to estimate current levels of gene flow. Divergence time estimates suggest that European populations began diverging about 60,000 years before present. The relatively recent divergence of populations in North Africa, Italy, and Iberia may explain why classic migration estimates based on equilibrium assumptions are high for these populations. We compare these estimates with nonequilibrium-based estimates and show that the nonequilibrium estimates are consistently lower than the equilibrium estimates. [source] CONTEMPORARY ISOLATION-BY-DISTANCE, BUT NOT ISOLATION-BY-TIME, AMONG DEMES OF EUROPEAN GRAYLING (THYMALLUS THYMALLUS, LINNAEUS) WITH RECENT COMMON ANCESTORSEVOLUTION, Issue 2 2009Nicola J. Barson The development of isolation by distance (IBD) and isolation by time (IBT) was contrasted among demes of European grayling (Thymallus thymallus) that have diverged within the last 25 generations following colonization of a lake (Lesjaskogsvatnet). We find low but significant levels of genetic differentiation among spawning tributaries and a pattern of IBD among them. We do not, however, find evidence for IBT despite an up to four-week difference in spawning date between "warm/early" and "cold/late" spawning demes and differences in the incubation temperatures experienced by offspring. It appears that IBD has developed more rapidly than IBT in this system and that adaptive divergence has been initiated in the absence of IBT. Although analysis of selected loci could reveal reduced recombination in parts of the genome associated with temporal divergence, our analysis of neutral genetic data suggests that IBD is a more important isolating mechanism in the early stages of adaptive divergence in European grayling. [source] One of the duplicated matrix metalloproteinase-9 genes is expressed in regressing tail during anuran metamorphosisDEVELOPMENT GROWTH & DIFFERENTIATION, Issue 4 2006Kenta Fujimoto The drastic morphological changes of the tadpole are induced during the climax of anuran metamorphosis, when the concentration of endogenous thyroid hormone is maximal. The tadpole tail, which is twice as long as the body, shortens rapidly and disappears completely in several days. We isolated a cDNA clone, designated as Xl MMP-9TH, similar to the previously reported Xenopus laevis MMP-9 gene, and showed that their Xenopus tropicalis counterparts are located tandemly about 9 kb apart from each other in the genome. The Xenopus MMP-9TH gene was expressed in the regressing tail and gills and the remodeling intestine and central nervous system, and induced in thyroid hormone-treated tail-derived myoblastic cultured cells, while MMP-9 mRNA was detected in embryos. Three thyroid hormone response elements in the distal promoter and the first intron were involved in the upregulation of the Xl MMP-9TH gene by thyroid hormone in transient expression assays, and their relative positions are conserved between X. laevis and X. tropicalis promoters. These data strongly suggest that the MMP-9 gene was duplicated, and differentiated into two genes, one of which was specialized in a common ancestor of X. laevis and X. tropicalis to be expressed in degenerating and remodeling organs as a response to thyroid hormone during metamorphosis. [source] Comparative expression analysis of transcription factor genes in the endostyle of invertebrate chordatesDEVELOPMENTAL DYNAMICS, Issue 3 2005Jin Hiruta Abstract The endostyle of invertebrate chordates is a pharyngeal organ that is thought to be homologous with the follicular thyroid of vertebrates. Although thyroid-like features such as iodine-concentrating and peroxidase activities are located in the dorsolateral part of both ascidian and amphioxus endostyles, the structural organization and numbers of functional units are different. To estimate phylogenetic relationships of each functional zone with special reference to the evolution of the thyroid, we have investigated, in ascidian and amphioxus, the expression patterns of thyroid-related transcription factors such as TTF-2/FoxE4 and Pax2/5/8, as well as the forkhead transcription factors FoxQ1 and FoxA. Comparative gene expression analyses depicted an overall similarity between ascidians and amphioxus endostyles, while differences in expression patterns of these genes might be specifically related to the addition or elimination of a pair of glandular zones. Expressions of Ci-FoxE and BbFoxE4 suggest that the ancestral FoxE class might have been recruited for the formation of thyroid-like region in a possible common ancestor of chordates. Furthermore, coexpression of FoxE4, Pax2/5/8, and TPO in the dorsolateral part of both ascidian and amphioxus endostyles suggests that genetic basis of the thyroid function was already in place before the vertebrate lineage. Developmental Dynamics 233:1031,1037, 2005. © 2005 Wiley-Liss, Inc. [source] An amphioxus winged helix/forkhead gene, AmphiFoxD: Insights into vertebrate neural crest evolutionDEVELOPMENTAL DYNAMICS, Issue 3 2002Jr-Kai Yu Abstract During amphioxus development, the neural plate is bordered by cells expressing many genes with homologs involved in vertebrate neural crest induction. However, these amphioxus cells evidently lack additional genetic programs for the cell delaminations, migrations, and differentiations characterizing definitive vertebrate neural crest. We characterize an amphioxus winged helix/forkhead gene (AmphiFoxD) closely related to vertebrate FoxD genes. Phylogenetic analysis indicates that the AmphiFoxD is basal to vertebrate FoxD1, FoxD2, FoxD3, FoxD4, and FoxD5. One of these vertebrate genes (FoxD3) consistently marks neural crest during development. Early in amphioxus development, AmphiFoxD is expressed medially in the anterior neural plate as well as in axial (notochordal) and paraxial mesoderm; later, the gene is expressed in the somites, notochord, cerebral vesicle (diencephalon), and hindgut endoderm. However, there is never any expression in cells bordering the neural plate. We speculate that an AmphiFoxD homolog in the common ancestor of amphioxus and vertebrates was involved in histogenic processes in the mesoderm (evagination and delamination of the somites and notochord); then, in the early vertebrates, descendant paralogs of this gene began functioning in the presumptive neural crest bordering the neural plate to help make possible the delaminations and cell migrations that characterize definitive vertebrate neural crest. © 2002 Wiley-Liss, Inc. [source] The evolution of the protonephridial terminal organ across Rotifera with particular emphasis on Dicranophorus forcipatus, Encentrum mucronatum and Erignatha clastopis (Rotifera: Dicranophoridae)ACTA ZOOLOGICA, Issue 2 2010Ole Riemann Abstract Riemann, O. and Ahlrichs, W.H. 2009. The evolution of the protonephridial terminal organ across Rotifera with particular emphasis on Dicranophorus forcipatus, Encentrum mucronatum and Erignatha clastopis (Rotifera: Dicranophoridae). ,Acta Zoologica (Stockholm) 91: 199,211 We report on the ultrastructure of the protonephridial terminal organ in three species of dicranophorid rotifers (Dicranophorus forcipatus, Encentrum mucronatum and Erignatha clastopis). Differences between the three species relate to shape and size, the morphology of the filter region and the number of microvilli and cilia inside the terminal organ. A comparison across Rotifera indicates that the terminal organs in D. forcipatus display a number of plesiomorphic characters, but are modified in E. mucronatum and Er. clastopis. This is in accordance with the results of phylogenetic analyses suggesting a basal position of D. forcipatus compared with the more derived species E. mucronatum and Er. clastopis. Moreover, we survey available data on the terminal organ in Rotifera and discuss its evolutionary transformations. The protonephridial terminal organ in the common ancestor of Rotifera consisted of a cytoplasmic cylinder with cilia united into a vibratile flame and a single circle of circumciliary microvilli. Depending on the topology on which characters are optimized, the site of ultrafiltration was formed by longitudinal cytoplasmic columns spanned by a fine filter diaphragm or by pores in the wall of the terminal organ. In several taxa of Rotifera, the terminal organ , probably independently , lost its circumciliary microvilli. [source] Lateral transmission of equine arteritis virus among Lipizzaner stallions in South AfricaEQUINE VETERINARY JOURNAL, Issue 6 2003A. J. GUTHRIE Summary Reasons for performing study:A serological study conducted in 1995 revealed that 7 stallions at the Lipizzaner Centre, Gauteng, South Africa, were seropositive for antibody to equine arteritis virus (EAV). A Lipizzaner stallion imported into South Africa from Yugoslavia in 1981 had previously (1988) been confirmed to be an EAV carrier. Despite being placed under life-long breeding quarantine, EAV had been transmitted between stallions at the Lipizzaner Centre. Objectives: To investigate the phylogenetic relationships between the strain of EAV shed in the semen of the original carrier stallion and strains recovered from the semen of 5 other stallions; and to investigate the means whereby lateral transmission of EAV occurred among 7 in-contact, nonbreeding stallions at the Centre. Methods: EAV was isolated from semen collected from the seropositive stallions using RK-13 cells. Viral RNA was reverse transcribed and amplified by polymerase chain reaction using ORF5-specific primers, subjected to sequence and phylogenetic analysis. Results: Phylogenetic analysis of strains of EAV recovered from the semen of 6 persistently infected stal lions confirmed that all viruses were closely related and probably derived from a common ancestor, i.e. the stallion imported from Yugoslavia. Lateral transmission subsequently occurred among 7 in-contact, nonbreeding stallions at the Centre. It is speculated that these stallions may have been exposed to virus from be dding or fo mites contaminated with semen. Conclusions: These data confirm that lateral transmission of EAV can occur from shedding stallions to susceptible, in-contact horses, including other stallions, which may become persistently infected with the virus. Potential relevance: The findings are consistent with lateral spread of a single, unique strain of EAV among a group; and suggest that transmission of EAV may be initiated by infection of one or more stallions with virus on bedding or other fomites contaminated with EAV-infected semen. [source] INCIPIENT EVOLUTION OF WOLBACHIA COMPATIBILITY TYPESEVOLUTION, Issue 9 2004Sylvain Charlat Abstract . -Cytoplasmic incompatibility (CI) is induced in arthropods by the maternally inherited bacterium Wolbachia. When infected males mate with uninfected females or with females bearing a different Wolbachia variant, paternal chromosomes behave abnormally and embryos die. This pattern can be interpreted as resulting from two bacterial effects: One (usually termed mod, for modification) would affect sperm and induce embryo death, unless Wolbachia is also present in the egg, which implies the existence of a second effect, usually termed resc, for rescue. The fact that CI can occur in crosses between males and females infected by different Wolbachia shows that mod and resc interact in a specific manner. In other words, different compatibility types, or mod/resc pairs seem to have diverged from one (or a few) common ancestor(s). We are interested in the process allowing the evolution of mod/resc pairs. Here this question is addressed experimentally after cytoplasmic injection into a single host species (Drosophila simulans) by investigating compatibility relationships between closely related Wolbachia variants naturally evolving in different dipteran hosts: D. simulans, Drosophila melanogaster, and Rhagoletis cerasi. Our results suggest that closely related bacteria can be totally or partially incompatible. The compatibility relationships observed can be explained using a formal description of the mod and resc functions, implying both qualitative and quantitative variations. [source] THE SHAPES OF NEUTRAL GENE GENEALOGIES IN TWO SPECIES: PROBABILITIES OF MONOPHYLY, PARAPHYLY, AND POLYPHYLY IN A COALESCENT MODELEVOLUTION, Issue 7 2003Noah A. Rosenberg Abstract., The genealogies of samples of orthologous regions from multiple species can be classified by their shapes. Using a neutral coalescent model of two species, I give exact probabilities of each of four possible genealogical shapes: reciprocal monophyly, two types of paraphyly, and polyphyly. After the divergence that forms two species, each of which has population size N, polyphyly is the most likely genealogical shape for the lineages of the two species. At , 1.300N generations after divergence, paraphyly becomes most likely, and reciprocal monophyly becomes most likely at ,1.665N generations. For a given species, the time at which 99% of its loci acquire monophyletic genealogies is ,5.298N generations, assuming all loci in its sister species are monophyletic. The probability that all lineages of two species are reciprocally monophyletic given that a sample from the two species has a reciprocally monophyletic genealogy increases rapidly with sample size, as does the probability that the most recent common ancestor (MRCA) for a sample is also the MRCA for all lineages from the two species. The results have potential applications for the testing of evolutionary hypotheses. [source] TIME TO THE MOST RECENT COMMON ANCESTOR AND DIVERGENCE TIMES OF POPULATIONS OF COMMON CHAFFINCHES (FRINGILLA COELEBS) IN EUROPE AND NORTH AFRICA: INSIGHTS INTO PLEISTOCENE REFUGIA AND CURRENT LEVELS OF MIGRATIONEVOLUTION, Issue 1 2002Cortland K. Griswold Abstract We analyzed sequences from a 275-bp hypervariable region in the 5, end of the mitochondrial DNA control region in 190 common chaffinches (Fringilla coelebs) from 19 populations in Europe and North Africa, including new samples from Greece and Morocco. Coalescent techniques were applied to estimate the time to the most recent common ancestor (TMRCA) and divergence times of these populations. The first objective of this study was to infer the locations of refugia where chaffinches survived the last glacial episode, and this was achieved by estimating the TMRCA of populations in regions surrounding the Mediterranean that were unglaciated in the late Pleistocene. Although extant populations in Iberia, Corsica, Greece, and North Africa harbor haplotypes that are basal in a phylogenetic tree, this information alone cannot be used to infer that these localities served as refugia, because it is impossible to infer the ages of populations and their divergence times without also considering the population genetic processes of mutation, migration, and drift. Provided we assume the TMRCAs of populations are a reasonable estimate of a population's age, coalescent-based methods place resident populations in Iberia, Corsica, Greece, and North Africa during the time of the last glacial maximum, suggesting these regions served as refugia for the common chaffinch. The second objective was to determine when populations began diverging from each other and to use this as a baseline to estimate current levels of gene flow. Divergence time estimates suggest that European populations began diverging about 60,000 years before present. The relatively recent divergence of populations in North Africa, Italy, and Iberia may explain why classic migration estimates based on equilibrium assumptions are high for these populations. We compare these estimates with nonequilibrium-based estimates and show that the nonequilibrium estimates are consistently lower than the equilibrium estimates. [source] DIVERGENCE WITH GENE FLOW IN THE ROCK-DWELLING CICHLIDS OF LAKE MALAWIEVOLUTION, Issue 5 2000Patrick D. Danley Abstract Within the past two million years, more than 450 species of haplochromine cichlids have diverged from a single common ancestor in Lake Malawi. Several factors have been implicated in the diversification of this monophyletic clade, including changes in lake level and low levels of gene flow across limited geographic scales. The objectives of this study were to determine the effect of recent lake-level fluctuations on patterns of allelic diversity in the genus Metriaclima, to describe the patterns of population structure within this genus, and to identify barriers to migration. This was accomplished through an analysis of allele frequencies at four microsatellite loci. Twelve populations spanning four species within Metriaclima were surveyed. The effect of lake-level fluctuations can be seen in the reduced genetic diversity of the most recently colonized sites; however, genetic diversity is not depressed at the species level. Low levels of population structure exist among populations, yet some gene flow persists across long stretches of inhospitable habitat. No general barrier to migration was identified. The results of this study are interpreted with respect to several speciation models. Divergence via population bottlenecks is unlikely due to the large allelic diversity observed within each species. Genetic drift and microallopatric divergence are also rejected because some gene flow does occur between adjacent populations. However, the reduced levels of gene flow between populations does suggest that minor changes in the selective environment could cause the divergence of populations. [source] Tracking the origins of the bilaterian Hox patterning system: insights from the acoel flatworm Symsagittifera roscoffensisEVOLUTION AND DEVELOPMENT, Issue 5 2009Eduardo Moreno SUMMARY Genes of the Hox cluster encode for transcriptional regulators that show collinear expression along the anteroposterior (AP) body axis in all bilateral animals. However, it is still unclear when in the evolutionary history of bilaterians the Hox system first conferred positional identity along the AP-axis. Recent molecular phylogenies have convincingly shown that the acoel flatworms, traditionally classified within the Platyhelminthes, are the sister group of the remaining Bilateria, branching out before the common ancestor of protostomes, and deuterostomes (the so-called PDA). This key phylogenetic position offers the opportunity to search for the presence and early role of Hox cluster genes to pattern the AP axis in acoels. Here, we report on the cloning, genomic arrangement, and expression domains of Hox genes in Symsagittifera roscoffensis. Three Hox genes were detected: one from each of the major groups of Hox genes, which are anterior, central, and posterior. In bacterial artificial chromosome cloning, sequencing, and chromosomal fluorescence in situ hybridization, Hox genes were not observed as being clustered in a unique genomic region. Nevertheless, despite its dispersion within the genome, Hox genes are expressed in nested domains along the AP axis in the juvenile worm. The basic set of Hox genes in acoels and their coarse nested spatial deployment might be the first indicators of the role of Hox genes in the evolution of bilateral symmetry and AP positional identity from a hypothetical radial ancestor. [source] The amphioxus T-box gene, AmphiTbx15/18/22, illuminates the origins of chordate segmentationEVOLUTION AND DEVELOPMENT, Issue 2 2006Laura Beaster-Jones SUMMARY Amphioxus and vertebrates are the only deuterostomes to exhibit unequivocal somitic segmentation. The relative simplicity of the amphioxus genome makes it a favorable organism for elucidating the basic genetic network required for chordate somite development. Here we describe the developmental expression of the somite marker, AmphiTbx15/18/22, which is first expressed at the mid-gastrula stage in dorsolateral mesendoderm. At the early neurula stage, expression is detected in the first three pairs of developing somites. By the mid-neurula stage, expression is downregulated in anterior somites, and only detected in the penultimate somite primordia. In early larvae, the gene is expressed in nascent somites before they pinch off from the posterior archenteron (tail bud). Integrating functional, phylogenetic and expression data from a variety of triploblast organisms, we have reconstructed the evolutionary history of the Tbx15/18/22 subfamily. This analysis suggests that the Tbx15/18/22 gene may have played a role in patterning somites in the last common ancestor of all chordates, a role that was later conserved by its descendents following gene duplications within the vertebrate lineage. Furthermore, the comparison of expression domains within this gene subfamily reveals similarities in the genetic bases of trunk and cranial mesoderm segmentation. This lends support to the hypothesis that the vertebrate head evolved from an ancestor possessing segmented cranial mesoderm. [source] Generality of vertebrate developmental patterns: evidence for a dermomyotome in fishEVOLUTION AND DEVELOPMENT, Issue 1 2006S. H. Devoto SUMMARY The somitic compartment that gives rise to trunk muscle and dermis in amniotes is an epithelial sheet on the external surface of the somite, and is known as the dermomyotome. However, despite its central role in the development of the trunk and limbs, the evolutionary history of the dermomyotome and its role in nonamniotes is poorly understood. We have tested whether a tissue with the morphological and molecular characteristics of a dermomyotome exists in nonamniotes. We show that representatives of the agnathans and of all major clades of gnathostomes each have a layer of cells on the surface of the somite, external to the embryonic myotome. These external cells do not show any signs of terminal myogenic or dermogenic differentiation. Moreover, in the embryos of bony fishes as diverse as sturgeons (Chondrostei) and zebrafish (Teleostei) this layer of cells expresses the pax3 and pax7 genes that mark myogenic precursors. Some of the pax7- expressing cells also express the differentiation-promoting myogenic regulatory factor Myogenin and appear to enter into the myotome. We therefore suggest that the dermomyotome is an ancient and conserved structure that evolved prior to the last common ancestor of all vertebrates. The identification of a dermomyotome in fish makes it possible to apply the powerful cellular and genetic approaches available in zebrafish to the understanding of this key developmental structure. [source] Characterization of novel GPCR gene coding locus in amphioxus genome: Gene structure, expression, and phylogenetic analysis with implications for its involvement in chemoreceptionGENESIS: THE JOURNAL OF GENETICS AND DEVELOPMENT, Issue 2 2005Gouki Satoh Abstract Chemosensation is the primary sensory modality in almost all metazoans. The vertebrate olfactory receptor genes exist as tandem clusters in the genome, so that identifying their evolutionary origin would be useful for understanding the expansion of the sensory world in relation to a large-scale genomic duplication event in a lineage leading to the vertebrates. In this study, I characterized a novel GPCR (G-protein-coupled receptor) gene-coding locus from the amphioxus genome. The genomic DNA contains an intronless ORF whose deduced amino acid sequence encodes a seven-transmembrane protein with some amino acid residues characteristic of vertebrate olfactory receptors (ORs). Surveying counterparts in the Ciona intestinalis (Asidiacea, Urochordata) genome by querying BLAST programs against the Ciona genomic DNA sequence database resulted in the identification of a remotely related gene. In situ hybridization analysis labeled primary sensory neurons in the rostral epithelium of amphioxus adults. Based on these findings, together with comparison of the developmental gene expression between amphioxus and vertebrates, I postulate that chemoreceptive primary sensory neurons in the rostrum are an ancient cell population traceable at least as far back in phylogeny as the common ancestor of amphioxus and vertebrates. genesis 41:47,57, 2005. © 2005 Wiley-Liss, Inc. [source] Hypotheses for the origin and early evolution of triterpenoid cyclasesGEOBIOLOGY, Issue 1 2007W. W. FISCHER ABSTRACT Hopanes and steranes are found almost universally in the sedimentary rock record where they often are used as proxies for aerobic organisms, metabolisms, and environments. In order to interpret ancient lipid signatures confidently we require a complementary understanding of how these modern biochemical pathways evolved since their conception. For example, generally it has been assumed that hopanoid biosynthesis was an evolutionary predecessor to steroid biosynthesis. Here we re-evaluate this assumption. Using a combined phylogenetic and biochemical perspective, we address the evolution of polycyclic triterpenoid biosynthesis and suggest several constraints on using these molecules as aerobic biomarkers. Amino acid sequence data show that the enzymes responsible for polycyclic triterpenoid biosynthesis (i.e. squalene and 2,3-oxidosqualene cyclases) are homologous. Numerous conserved domains correspond to active sites in the enzymes that are required to complete the complex cyclization reaction. From these sites we develop an evolutionary analysis of three independent characters to explain the evolution of the major classes of polycyclic triterpenoids. These characters are: (i) the number of unfavourable anti-Markovnikov ring closures, (ii) all-chair (CCC) or chair-boat-chair (CBC) substrate conformation, and (iii) the choice between squalene and 2,3-oxidosqualene as the substrate. We use these characters to construct four competing phylogenies to describe the evolution of polycyclic triterpenoid biosynthesis. The analysis suggests that malabaricanoids would be the most ancient polycyclic triterpenoids. The two most parsimonious evolutionary trees are the ones in which hopanoid and steroid cyclases diverged from a common ancestor. The transition from a CCC- to CBC-fold marks the major divergence in the evolution of these pathways, and it is diagnosable in the geological record. However, this transition does not require the simultaneous adoption of the aerobic substrate, 2,3-oxidosqualene, because these characters are controlled by independent parts of the enzyme. [source] Geobiological analysis using whole genome-based tree building applied to the Bacteria, Archaea, and EukaryaGEOBIOLOGY, Issue 1 2003Christopher H. House ABSTRACT We constructed genomic trees based on the presence and absence of families of protein-encoding genes observed in 55 prokaryotic and five eukaryotic genomes. There are features of the genomic trees that are not congruent with typical rRNA phylogenetic trees. In the bacteria, for example, Deinococcus radiodurans associates with the Gram-positive bacteria, a result that is also seen in some other phylogenetic studies using whole genome data. In the Archaea, the methanogens plus Archaeoglobus form a united clade and the Euryarchaeota are divided with the two Thermoplasma genomes and Halobacterium sp. falling below the Crenarchaeota. While the former appears to be an accurate representation of methanogen-relatedness, the misplacement of Halobacterium may be an artefact of parsimony. These results imply the last common ancestor of the Archaea was not a methanogen, leaving sulphur reduction as the most geochemically plausible metabolism for the base of the archaeal crown group. It also suggests that methanogens were not a component of the Earth's earliest biosphere and that their origin occurred sometime during the Archean. In the Eukarya, the parsimony analysis of five Eukaryotes using the Crenarchaeota as an outgroup seems to counter the Ecdysozoa hypothesis, placing Caenorhabditis elegans (Nematoda) below the common ancestor of Drosophila melanogaster (Arthropoda) and Homo sapiens (Chordata) even when efforts are made to counter the possible effects of a faster rate of sequence evolution for the C. elegans genome. Further analysis, however, suggests that the gene loss of ,animal' genes is highest in C. elegans and is obscuring the relationships of these organisms. [source] The pre-radial history of echinodermsGEOLOGICAL JOURNAL, Issue 3 2005Andrew B. Smith Abstract Gene sequence data now identify a robust phylogeny of deuterostomes and provide a framework within which the evolution of echinoderms can be interpreted. The topology of the molecular tree makes a number of important predictions about the morphological characters of the earliest echinoderm at its split from hemichordates: it possessed gill slits (but not a notochord), had a bilaterally symmetrical body plan in the adult and, less certainly, underwent torsion during development. Carpoids, a highly contentious group of extinct deuterostomes with a plated calcite skeleton that have variously been interpreted as stem- and crown-group chordates, stem-group echinoderms or stem- and crown-group echinoderms, display many of these basal characters and provide critical evidence for how the latest common ancestor of hemichordates and echinoderms was transformed into a pentaradiate crown-group echinoderm. Cinctans have a large atrial opening in addition to mouth and anus, and are interpreted as pharyngeal basket feeders. The paired grooves associated with the mouth indicate the presence of a hydrovascular system, but not necessarily one built along the echinoderm plan (that is, derived from just the left hydrocoel). Stylophorans have a bilateral body plan that is externally masked by torsion and possess gills, either unpaired and external, or paired and internal, opening into an atrial cavity. Their bilateral appendage is a locomotory organ, not an ambulacrum, and there is no evidence that stylophorans ever possessed a well-developed hydrovascular system homologous to the water vascular system of echinoderms and the tentacles of pterobranch hemichordates. Solutes are the most crownward, having a true echinodermal ambulacral system with a single hydropore and no pharyngeal gill openings. Copyright © 2005 John Wiley & Sons, Ltd. [source] Syndrome-causing mutations of the BLM gene in persons in the Bloom's Syndrome Registry,,HUMAN MUTATION, Issue 8 2007James German Abstract Bloom syndrome (BS) is caused by homozygous or compound heterozygous mutations in the RecQ DNA helicase gene BLM. Since the molecular isolation of BLM, characterization of BS-causing mutations has been carried out systematically using samples stored in the Bloom's Syndrome Registry. In a survey of 134 persons with BS from the Registry, 64 different mutations were identified in 125 of them, 54 that cause premature protein-translation termination and 10 missense mutations. In 102 of the 125 persons in whom at least one BLM mutation was identified, the mutation was recurrent, that is, it was shared by two or more persons with BS; 19 of the 64 different mutations were recurrent. Ethnic affiliations of the persons who carry recurrent mutations indicate that the majority of such persons inherit their BLM mutation identical-by-descent from a recent common ancestor, a founder. The presence of widespread founder mutations in persons with BS points to population genetic processes that repeatedly and pervasively generate mutations that recur in unrelated persons. Hum Mutat 28(8), 743,753, 2007. Published 2007 Wiley-Liss, Inc. [source] Sarcoglycanopathies and the risk of undetected deletion alleles in diagnosis,,HUMAN MUTATION, Issue 1 2005Stefan J. White Abstract We have designed Multiplex Amplifiable Probe Hybridization (MAPH) probes for 28 exons of the sarcoglycan genes SGCA, SGCB, SGCG, and SGCD. The set was used to screen DNA from limb-girdle muscular dystrophy (LGMD) patients for the presence of pathogenic deletion or duplication mutations. An unexpected heterozygous deletion of SGCG exon 7 was detected in a patient from a consanguineous family in which a known c.525delT mutation segregates. The exon 7 deletion was inherited from the father, who was part of the consanguineous c.525delT branch of the family but who did not carry the c.525delT mutation. A similar, homozygous deletion had been identified in two unrelated LGMD patients from southern Italy. The deletion breakpoints were mapped, isolated, and sequenced, and were identical in all cases. Haplotype analysis showed the same alleles segregating with the mutation in all three patients, suggesting a common ancestor. Exonic deletions in sarcoglycanopathies appear to be rare events. However, we recommend screening for exonic deletions/duplications in patients where a mutation has not been identified in both alleles, as well as in seemingly homozygous cases where segregation of the mutations can not be confirmed in the parents. © 2005 Wiley-Liss, Inc. [source] Evidence of a founder mutation of BRCA1 in a highly homogeneous population from southern Italy with breast/ovarian cancerHUMAN MUTATION, Issue 2 2001Francesco Baudi Abstract Several genes have been involved in the pathogenesis of hereditary breast/ovarian cancer (BOC), but mutations in the BRCA1 gene are by far the most recurrent. In this study, we report the identification of a founder mutation in a geographically and historically homogeneous population from Calabria, a south Italian region. A screening performed on 24 patients from unrelated families highlighted the high prevalence of a 5083del19 alteration in the BRCA1 gene, which accounts for 33% of the overall gene mutations. The same mutation was also detected in 4 patients, all of Calabrian origin, referred to us by research centres from the north of Italy. Allelotype analysis, performed on probands and unaffected family members revealed the presence a common allele, therefore suggesting a founder effect due to a common ancestor. Our findings underscore the importance of ethnic background homogeneity in patients' selection and highlight the usefulness of founder mutations as a potential tool for optimisation of preclinical diagnosis in gene carriers and therapeutic approaches in affected individuals. Hum Mutat 18:163,164, 2001. © 2001 Wiley-Liss, Inc. [source] Evolutionary analysis of fructose 2,6-bisphosphate metabolismIUBMB LIFE, Issue 3 2006Paul A. M. Michels Abstract Fructose 2,6-bisphosphate is a potent metabolic regulator in eukaryotic organisms; it affects the activity of key enzymes of the glycolytic and gluconeogenic pathways. The enzymes responsible for its synthesis and hydrolysis, 6-phosphofructo-2-kinase (PFK-2) and fructose-2,6-bisphosphatase (FBPase-2) are present in representatives of all major eukaryotic taxa. Results from a bioinformatics analysis of genome databases suggest that very early in evolution, in a common ancestor of all extant eukaryotes, distinct genes encoding PFK-2 and FBPase-2, or related enzymes with broader substrate specificity, fused resulting in a bifunctional enzyme both domains of which had, or later acquired, specificity for fructose 2,6-bisphosphate. Subsequently, in different phylogenetic lineages duplications of the gene of the bifunctional enzyme occurred, allowing the development of distinct isoenzymes for expression in different tissues, at specific developmental stages or under different nutritional conditions. Independently in different lineages of many unicellular eukaryotes one of the domains of the different PFK-2/FBPase-2 isoforms has undergone substitutions of critical catalytic residues, or deletions rendering some enzymes monofunctional. In a considerable number of other unicellular eukaryotes, mainly parasitic organisms, the enzyme seems to have been lost altogether. Besides the catalytic core, the PFK-2/FBPase-2 has often N- and C-terminal extensions which show little sequence conservation. The N-terminal extension in particular can vary considerably in length, and seems to have acquired motifs which, in a lineage-specific manner, may be responsible for regulation of catalytic activities, by phosphorylation or ligand binding, or for mediating protein-protein interactions. IUBMB Life, 58: 133 - 141, 2006 [source] The Evolution of the Human Self: Tracing the Natural History of Self-AwarenessJOURNAL FOR THE THEORY OF SOCIAL BEHAVIOUR, Issue 4 2003Mark R. Leary Previous discussions of the evolution of the self have diverged greatly in their estimates of the date at which the capacity for self-thought emerged, the factors that led self-reflection to evolve, and the nature of the evidence offered to support these disparate conclusions. Beginning with the assumption that human self-awareness involves a set of distinct cognitive abilities that evolved at different times to solve different adaptive problems, we trace the evolution of self-awareness from the common ancestor of humans and apes to the beginnings of culture, drawing upon paleontological, anthropological, biological, and psychological evidence. These data converge to suggest that that modern self-thought appeared just prior to the Middle-Upper Paleolithic transition, approximately 60,000 years ago.Recto running head: Evolution of the Self. [source] Evolution of the vertebrate jaw: comparative embryology and molecular developmental biology reveal the factors behind evolutionary noveltyJOURNAL OF ANATOMY, Issue 5 2004Shigeru Kuratani Abstract It is generally believed that the jaw arose through the simple transformation of an ancestral rostral gill arch. The gnathostome jaw differentiates from Hox -free crest cells in the mandibular arch, and this is also apparent in the lamprey. The basic Hox code, including the Hox -free default state in the mandibular arch, may have been present in the common ancestor, and jaw patterning appears to have been secondarily constructed in the gnathostomes. The distribution of the cephalic neural crest cells is similar in the early pharyngula of gnathostomes and lampreys, but different cell subsets form the oral apparatus in each group through epithelial,mesenchymal interactions: and this heterotopy is likely to have been an important evolutionary change that permitted jaw differentiation. This theory implies that the premandibular crest cells differentiate into the upper lip, or the dorsal subdivision of the oral apparatus in the lamprey, whereas the equivalent cell population forms the trabecula of the skull base in gnathostomes. Because the gnathostome oral apparatus is derived exclusively from the mandibular arch, the concepts ,oral' and ,mandibular' must be dissociated. The ,lamprey trabecula' develops from mandibular mesoderm, and is not homologous with the gnathostome trabecula, which develops from premandibular crest cells. Thus the jaw evolved as an evolutionary novelty through tissue rearrangements and topographical changes in tissue interactions. [source] A long-standing Pleistocene refugium in southern Africa and a mosaic of refugia in East Africa: insights from mtDNA and the common eland antelopeJOURNAL OF BIOGEOGRAPHY, Issue 3 2010Eline D. Lorenzen Abstract Aim, Previous genetic studies of African savanna ungulates have indicated Pleistocene refugial areas in East and southern Africa, and recent palynological, palaeovegetation and fossil studies have suggested the presence of a long-standing refugium in the south and a mosaic of refugia in the east. Phylogeographic analysis of the common eland antelope, Taurotragus oryx (Bovidae), was used to assess these hypotheses and the existence of genetic signatures of Pleistocene climate change. Location, The sub-Saharan savanna biome of East and southern Africa. Methods, Mitochondrial DNA control-region fragments (414 bp) from 122 individuals of common eland were analysed to elucidate the phylogeography, genetic diversity, spatial population structuring, historical migration and demographic history of the species. The phylogeographic split among major genetic lineages was dated using Bayesian coalescent-based methods and a calibrated fossil root of 1.6 Ma for the split between the common eland and the giant eland, Taurotragus derbianus. Results, Two major phylogeographic lineages comprising East and southern African localities, respectively, were separated by a net nucleotide distance of 4.7%. A third intermediate lineage comprised only three haplotypes, from Zimbabwe in southern Africa. The estimated mutation rate of 0.097 Myr,1 revealed a more recent common ancestor for the eastern lineage (0.21 Ma; 0.07,0.37) than for the southern lineage (0.35 Ma; 0.10,0.62). Compared with the latter, the eastern lineage showed pronounced geographic structuring, lower overall nucleotide diversity, higher population differentiation, and isolation-by-distance among populations. Main conclusions, The data support the hypothesis of Pleistocene refugia occurring in East and southern Africa. In agreement with palynological, palaeovegetation and fossil studies, our data strongly support the presence of a longer-standing population in the south and a mosaic of Pleistocene refugia in the east, verifying the efficacy of genetic tools in addressing such questions. The more recent origin of the common eland inhabiting East Africa could result from colonization following extinction from the region. Only two other dated African ungulate phylogenies have been published, applying different methods, and the similarity of dates obtained from the three distinct approaches indicates a significant event c. 200 ka, which left a strong genetic signature across a range of ungulate taxa. [source] Are the Northern Andes a species pump for Neotropical birds?JOURNAL OF BIOGEOGRAPHY, Issue 2 2010Phylogenetics, biogeography of a clade of Neotropical tanagers (Aves: Thraupini) Abstract Aim, We used mitochondrial DNA sequence data to reconstruct the phylogeny of a large clade of tanagers (Aves: Thraupini). We used the phylogeny of this Neotropical bird group to identify areas of vicariance, reconstruct ancestral zoogeographical areas and elevational distributions, and to investigate the correspondence of geological events to speciation events. Location, The species investigated are found in 18 of the 22 zoogeographical regions of South America, Central America and the Caribbean islands; therefore, we were able to use the phylogeny to address the biogeographical history of the entire region. Methods, Molecular sequence data were gathered from two mitochondrial markers (cytochrome b and ND2) and analysed using Bayesian and maximum-likelihood approaches. Dispersal,vicariance analysis (DIVA) was used to reconstruct zoogeographical areas and elevational distributions. A Bayesian framework was also used to address changes in elevation during the evolutionary history of the group. Results, Our phylogeny was similar to previous tanager phylogenies constructed using fewer species; however, we identified three genera that are not monophyletic and uncovered high levels of sequence divergence within some species. DIVA identified early diverging nodes as having a Northern Andean distribution, and the most recent common ancestor of the species included in this study occurred at high elevations. Most speciation events occurred either within highland areas or within lowland areas, with few exchanges occurring between the highlands and lowlands. The Northern Andes has been a source for lineages in other regions, with more dispersals out of this area relative to dispersals into this area. Most of the dispersals out of the Northern Andes were dispersals into the Central Andes; however, a few key dispersal events were identified out of the Andes and into other zoogeographical regions. Main conclusions, The timing of diversification of these tanagers correlates well with the main uplift of the Northern Andes, with the highest rate of speciation occurring during this timeframe. Central American tanagers included in this study originated from South American lineages, and the timing of their dispersal into Central America coincides with or post-dates the completion of the Panamanian isthmus. [source] Evolution of the second orangutan: phylogeny and biogeography of hominid originsJOURNAL OF BIOGEOGRAPHY, Issue 10 2009John R. Grehan Abstract Aim, To resolve the phylogeny of humans and their fossil relatives (collectively, hominids), orangutans (Pongo) and various Miocene great apes and to present a biogeographical model for their differentiation in space and time. Location, Africa, northern Mediterranean, Asia. Methods, Maximum parsimony analysis was used to assess phylogenetic relationships among living large-bodied hominoids (= humans, chimpanzees, bonobos, gorillas, orangutans), and various related African, Asian and European ape fossils. Biogeographical characteristics were analysed for vicariant replacement, main massings and nodes. A geomorphological correlation was identified for a clade we refer to as the ,dental hominoids', and this correlation was used to reconstruct their historical geography. Results, Our analyses support the following hypotheses: (1) the living large-bodied hominoids represent a monophyletic group comprising two sister clades: humans + orangutans, and chimpanzees (including bonobos) + gorillas (collectively, the African apes); and (2) the human,orangutan clade (dental hominoids) includes fossil hominids (Homo, australopiths, Orrorin) and the Miocene-age apes Hispanopithecus, Ouranopithecus, Ankarapithecus, Sivapithecus, Lufengpithecus, Khoratpithecus and Gigantopithecus (also Plio-Pleistocene of eastern Asia). We also demonstrate that the distributions of living and fossil genera are largely vicariant, with nodes of geographical overlap or proximity between Gigantopithecus and Sivapithecus in Central Asia, and between Pongo, Gigantopithecus, Lufengpithecus and Khoratpithecus in East Asia. The main massing is represented by five genera and eight species in East Asia. The dental hominoid track is spatially correlated with the East African Rift System (EARS) and the Tethys Orogenic Collage (TOC). Main conclusions, Humans and orangutans share a common ancestor that excludes the extant African apes. Molecular analyses are compromised by phenetic procedures such as alignment and are probably based on primitive retentions. We infer that the human,orangutan common ancestor had established a widespread distribution by at least 13 Ma. Vicariant differentiation resulted in the ancestors of hominids in East Africa and various primarily Miocene apes distributed between Spain and Southeast Asia (and possibly also parts of East Africa). The geographical disjunction between early hominids and Asian Pongo is attributed to local extinctions between Europe and Central Asia. The EARS and TOC correlations suggest that these geomorphological features mediated establishment of the ancestral range. [source] Mitochondrial DNA in Atherina (Teleostei, Atheriniformes): differential distribution of an intergenic spacer in lagoon and marine forms of Atherina boyeriJOURNAL OF FISH BIOLOGY, Issue 5 2008V. MILANA The big-scale sand smelt Atherina boyeri lives in fresh water, brackish water and sea water of the western Atlantic Ocean and Mediterranean Sea. Previous studies concerning distribution, biometric characters and genetic molecular markers have suggested the possible existence of two or even three different groups or species of sand smelt, one ,lagoon' type and one (or two , punctuated and non-punctuated on the flanks) ,marine' type. In this study, the presence and the localization of an insertion was described, c. 200 bp in length, in the mtDNA of the lagoon and marine punctuated specimens of A. boyeri and its absence in the marine non-punctuated specimens, as well as in other two congeneric species, Atherina hepsetus and Atherina presbyter, and in the atheriniform Menidia menidia. The intergenic spacer is located between the tRNAGlu and cytochrome b (cyt b) genes and shares a c. 50% sequence similarity with cyt b. The distribution and the features of the intergenic spacer suggest that it might have originated from an event of gene duplication, which involved the cyt b gene (or, more likely, a part of it) and which took place in the common ancestor of the lagoon and the marine punctuated specimens. The data obtained therefore support the hypothesis of the existence of three cryptic and, or sibling species within the A. boyeri taxon and provide a genetic molecular marker to distinguish them. [source] Genetic and morphological characterization of a Lake Ohrid endemic, Salmo (Acantholingua) ohridanus with a comparison to sympatric Salmo truttaJOURNAL OF FISH BIOLOGY, Issue A 2006S. Su Analysis of both uni-(two mtDNA gene sequences) and bi-parentally (seven microsatellite loci) inherited genetic markers, together with analysis of 40 morphological characters, described Salmo ohridanus as a highly divergent member of the genus Salmo. Based on comparative substitution rate differences at the cytochrome b gene, and a rough estimated age of the Salmo trutta complex (i.e. at least 2 million years), the S. ohridanus and Salmo obtusirostris clade probably split from a common ancestor of brown trout Salmo trutta >4 million years ago, overlapping with minimum age estimates of the formation of Europe's oldest freshwater habitat, Lake Ohrid. Comparative analysis with Lake Ohrid brown trout (known regionally as Salmo letnica), supported the notion that these fish have more recently colonized the lake and phylogenetically belong to the Adriatic lineage of brown trout. It is further suggested that species-specific saturation in the mtDNA control region underestimated the divergence between S. ohridanus and S. trutta. Evidence of rare hybridization between S. ohridanus and Lake Ohrid brown trout was seen at both mtDNA and microsatellite markers, but there was no support for extensive introgression. [source] The evolution of electroreception and bioelectrogenesis in teleost fish: a phylogenetic perspectiveJOURNAL OF FISH BIOLOGY, Issue 6 2001J. A. Alves-Gomes According to current phylogenetic theory, both electroreceptors and electric organs evolved multiple times throughout the evolution of teleosts. Two basic types of electroreceptors have been described: ampullary and tuberous electroreceptors. Ampullary-type electroreceptors appeared once in the common ancestor of the Siluriformes+Gymnotiformes (within the superorder Ostariophysi), and on two other occasions within the superorder Osteoglossomorpha: in the African Mormyriformes and in the African Notopteriformes. Tuberous receptors are assumed to have evolved three times; all within groups that already possessed ampullary receptors. With the exception of a single catfish species, for which studies are still lacking, all fish with tuberous electroreceptors also have an electric organ. Tuberous electroreceptors are found in the two unrelated electrogenic teleost lineages (orders Gymnotiformes and Mormyriformes) and in one non-electrogenic South American catfish species (order Siluriformes). Electric organs evolved eight times independently among teleosts: five of them among the ostariophysans (once in the gymnotiform ancestor and in four siluriform lineages), once in the common ancestor of Mormyriformes, and in two uranoscopids. With the exception of two uranoscopid genera, for which no electroreceptive capabilities have been discovered so far, all electric organs evolved as an extension of a pre-existing electroreceptive (ampullary) condition. It is suggested that plesiomorphic electric organ discharges (EODs) possessed a frequency spectrum that fully transgressed the tuning curve of ampullary receptors, i.e. a signal such as a long lasting monophasic pulse. Complex EOD waveforms appeared as a derived condition among electric fish. EODs are under constant evolutionary pressure to develop an ideal compromise between a function that enhances electrolocation and electrocommunication capabilities, and thereby ensures species identity through sexual and behavioural segregation, and minimizes the risk of predation. [source] | ||||||||||||||||||||||||||||||||||||||||||||||