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Evolutionary Tree (evolutionary + tree)

Distribution by Scientific Domains

Life Sciences	70%
Chemistry	20%

Selected Abstracts

Relation between domain evolution, specificity, and taxonomy of the ,-amylase family members containing a C-terminal starch-binding domain

FEBS JOURNAL, Issue 4 2003
tefan Jane
The ,-amylase family (glycoside hydrolase family 13; GH 13) contains enzymes with approximately 30 specificities. Six types of enzyme from the family can possess a C-terminal starch-binding domain (SBD): ,-amylase, maltotetraohydrolase, maltopentaohydrolase, maltogenic ,-amylase, acarviose transferase, and cyclodextrin glucanotransferase (CGTase). Such enzymes are multidomain proteins and those that contain an SBD consist of four or five domains, the former enzymes being mainly hydrolases and the latter mainly transglycosidases. The individual domains are labelled A [the catalytic (,/,)8 -barrel], B, C, D and E (SBD), but D is lacking from the four-domain enzymes. Evolutionary trees were constructed for domains A, B, C and E and compared with the ,complete-sequence tree'. The trees for domains A and B and the complete-sequence tree were very similar and contain two main groups of enzymes, an amylase group and a CGTase group. The tree for domain C changed substantially, the separation between the amylase and CGTase groups being shortened, and a new border line being suggested to include the Klebsiella and Nostoc CGTases (both four-domain proteins) with the four-domain amylases. In the ,SBD tree' the border between hydrolases (mainly,-amylases) and transglycosidases (principally CGTases) was not readily defined, because maltogenic ,-amylase, acarviose transferase, and the archaeal CGTase clustered together at a distance from the main CGTase cluster. Moreover the four-domain CGTases were rooted in the amylase group, reflecting sequence relationships for the SBD. It appears that with respect to the SBD, evolution in GH 13 shows a transition in the segment of the proteins C-terminal to the catalytic (,/,)8 -barrel(domain A). [source]

Gene trees: A powerful tool for exploring the evolutionary biology of species and speciation

PLANT SPECIES BIOLOGY, Issue 3 2000
Alan R. Templeton
Abstract Evolutionary trees can be constructed from the haplotypes observed with molecular surveys of sequence or restriction site variation. Such gene trees can be constructed regardless of whether or not all of the individual specimens came from one or many species. Hence, these gene trees can straddle the species/population interface, thereby providing a powerful tool for studying the meaning of species and the process of speciation. We illustrate how historical approaches using gene trees can be used to separate the effects of population structure from population history, in order to rigorously test the species status of a group, and to test hypotheses about the process of speciation. A worked example of species status in the Piriqueta caroliniana complex is presented. Species status is evaluated under the cohesion species concept that defines a species as an evolutionary lineage with boundaries arising from the forces that create reproductive communities. Such forces are collectively called cohesion mechanisms and consist of two main subtypes: (i) genetic exchangeability, and (ii) ecological interchangeability. To make this definition operational, populations that behave as separate evolutionary lineages are first identified. A method is reviewed for inferring lineages using explicit statistical criteria from geographic overlays upon gene trees. Once lineages have been identified, the next step is to use the cohesion mechanisms to identify candidate traits that should contribute to genetic exchangeability and/or ecological interchangeability. The cohesion species are then identified by performing overlays upon gene trees in order to identify significant transitions in the candidate traits. Cohesion species are recognized only when statistically significant reproductive/ecological transitions occur that are concordant with the lineages defined earlier. This data-rich method of recognizing species automatically generates much information about the biogeography, population structure, historical events, and ecology and/or reproductive biology of the group under study. In turn, this information provides much insight into the process of speciation. It also makes the criteria, data, methods of analysis and degree of support for the species inference completely explicit, thereby avoiding confusion, inconsistency and artificial controversies that plague much of the literature on species concepts. [source]

Microsatellite evolution in modern humans: a comparison of two data sets from the same populations

ANNALS OF HUMAN GENETICS, Issue 2 2000
L. JIN
We genotyped 64 dinucleotide microsatellite repeats in individuals from populations that represent all inhabited continents. Microsatellite summary statistics are reported for these data, as well as for a data set that includes 28 out of 30 loci studied by Bowcock et al. (1994) in the same individuals. For both data sets, diversity statistics such as heterozygosity, number of alleles per locus, and number of private alleles per locus produced the highest values in Africans, intermediate values in Europeans and Asians, and low values in Americans. Evolutionary trees of populations based on genetic distances separated groups from different continents. Corresponding trees were topologically similar for the two data sets, with the exception that the (,,)2 genetic distance reliably distinguished groups from different continents for the larger data set, but not for the smaller one. Consistent with our results from diversity statistics and from evolutionary trees, population growth statistics Sk and ,, which seem particularly useful for indicating recent and ancient population size changes, confirm a model of human evolution in which human populations expand in size and through space following the departure of a small group from Africa. [source]

Divergent roles of the DEAD-box protein BS-PL10, the urochordate homologue of human DDX3 and DDX3Y proteins, in colony astogeny and ontogeny

DEVELOPMENTAL DYNAMICS, Issue 6 2006
Amalia Rosner
Abstract Proteins of the highly conserved PL-10 (Ded1P) subfamily of DEAD-box family, participate in a wide variety of biological functions. However, the entire spectrum of their functions in both vertebrates and invertebrates is still unknown. Here, we isolated the Botryllus schlosseri (Urochordata) homologue, BS-PL10, revealing its distributions and functions in ontogeny and colony astogeny. In botryllid ascidians, the colony grows by increasing the number of modular units (each called a zooid) through a whole colony synchronized and weekly cyclical astogenic budding process (blastogenesis). At the level of the colony, both BS-PL10 mRNA and its protein (78 kDa) fluctuate in a weekly pattern that corresponds with the animal's blastogenic cycle, increasing from blastogenic stage A to blastogenic stage D. At the organ/module level, a sharp decline is revealed. Primary and secondary developing buds express high levels of BS-PL10 mRNA and protein at all blastogeneic stages. These levels are reduced four to nine times in the new set of functional zooids. This portrait of colony astogeny differed from its ontogeny. Oocytes and sperm cells express high levels of BS-PL10 protein only at early stages of development. Young embryos reveal background levels with increased expressions in some organs at more developed stages. Results reveal that higher levels of BS-PL10 mRNA and protein are characteristic to multipotent soma and germ cells, but patterns deviate between two populations of differentiating stem cells, the stem cells involved in weekly blastogenesis and stem cells involved in embryogenesis. Two types of experimental manipulations, zooidectomy and siRNA assays, have confirmed the importance of BS-PL10 for cell differentiation and organogenesis. BS-PL10 (phylogenetically matching the animal's position in the evolutionary tree), is the only member of this subfamily in B. schlosseri, featuring a wide range of biological activities, some of which represent pivotal roles. The surprising weekly cyclical expression and the participation in cell differentiation posit this molecule as a model system for studying PL10 protein subfamily. Developmental Dynamics 235:1508,1521, 2006. © 2006 Wiley-Liss, Inc. [source]

SEQUENCE ANALYSIS OF A NOVEL INSECT PHOSPHOGLYCERATE MUTASE GENE FROM THE CHINESE HONEYBEE, APIS CERANA,

INSECT SCIENCE, Issue 4 2003
Jiang-hong Li
Abstract A clone inserted with 1 104 bp fragment containing a 765bp Open Reading Frame(ORF), encoding a putative 2,3-bisphosphoglycerate(2,3BPG) dependent Phosphoglycerate mutase(dPGAM) that catalyzes the transfer of a phosphate group from the C3 carbon atom to the C2 carbon atom of phosphoglycerate, was screened by mass sequencing from the cDNA library of the venom glands of Apis cerana. The deduced amino acid sequence shared high similarities (39% - 88%)with the dPGAM of 7 other organisms, but the similarities with the iPGAM of 4 other organisms were low (10% - 12%). Moreover, the alignment of Ac-PGAM with the dPGAMs from 7 other organisms showed that all the active site amino acid residues were conserved. This result shows that Ac-PGAM is a typical dPGAM. Thus, this is the second PGAM gene reported in Insecta. Furthermore, phylogenetic analysis showed that the evolutionary tree of PGAMs reflects the systematic relationship of species. [source]

Haplotype Trees and Modern Human Origins

AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue S41 2005
Alan R. Templeton
Abstract A haplotype is a multisite haploid genotype at two or more polymorphic sites on the same chromosome in a defined DNA region. An evolutionary tree of the haplotypes can be estimated if the DNA region had little to no recombination. Haplotype trees can be used to reconstruct past human gene-flow patterns and historical events, but any single tree captures only a small portion of evolutionary history, and is subject to error. A fuller view of human evolution requires multiple DNA regions, and errors can be minimized by cross-validating inferences across loci. An analysis of 25 DNA regions reveals an out-of-Africa expansion event at 1.9 million years ago. Gene flow with isolation by distance was established between African and Eurasian populations by about 1.5 million years ago, with no detectable interruptions since. A second out-of-Africa expansion occurred about 700,000 years ago, and involved interbreeding with at least some Eurasian populations. A third out-of-Africa event occurred around 100,000 years ago, and was also characterized by interbreeding, with the hypothesis of a total Eurasian replacement strongly rejected (P < 10,17). This does not preclude the possibility that some Eurasian populations could have been replaced, and the status of Neanderthals is indecisive. Demographic inferences from haplotype trees have been inconsistent, so few definitive conclusions can be made at this time. Haplotype trees from human parasites offer additional insights into human evolution and raise the possibility of an Asian isolate of humanity, but once again not in a definitive fashion. Haplotype trees can also indicate which genes were subject to positive selection in the lineage leading to modern humans. Genetics provides many insights into human evolution, but those insights need to be integrated with fossil and archaeological data to yield a fuller picture of the origin of modern humans. Yrbk Phys Anthropol 48:33,59, 2005. © 2005 Wiley-Liss, Inc. [source]

Sound reasons for silence: why do molluscs not communicate acoustically?

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2010
GEERAT J. VERMEIJ
Many adaptively beneficial states of form, behaviour and physiology are absent in large parts of the evolutionary tree of life. Although the causes of these absences can never be fully known, insights into the possibilities and limitations of adaptive evolution can be gained by examining the conditions that would be necessary for the forbidden phenotypes to evolve. Here, the case of acoustic communication in molluscs is considered. The production of sound as a warning to predators or as a means to attract mates is widespread among arthropods and vertebrates, both on land and in water, but is unknown among molluscs, even though many derived clades of gastropods and cephalopods are characterized by internal fertilization and by the evolution of long-distance visual and chemical signalling. Many molluscs possess suitable hard parts , shell, operculum and jaws , for producing sound, but most shell-bearing molluscs lack the agility or aggression necessary to cope with high-activity enemies attracted to an acoustic beacon. Their evolutionary background, arising from the generally passive adaptations of molluscs and other animals with low metabolic rates, prevents selection favouring communication by sound, and indeed favours silence. Several clades of shell-bearing gastropods and cephalopods were identified in which sound production has the greatest potential to arise or to be discovered. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100, 485,493. [source]

Heterologous expression, crystallization and preliminary X-ray characterization of CcCel6C, a glycoside hydrolase family 6 enzyme from the basidiomycete Coprinopsis cinerea

ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 2 2009
Yuma Kurakata
CcCel6C is a gene that encodes a glycoside hydrolase family 6 (GH6) enzyme in the Coprinopsis cinerea genome. In the evolutionary tree of GH6 enzymes, the encoded enzyme was closely related to Cel6B from Humicola insolens, previously called endoglucanase VI, while its amino-acid sequence revealed a region corresponding to the C-terminal active-site-enclosing loop typical of cellobiohydrolase II. Here, the crystallization of CcCel6C produced in Escherichia coli is reported. The square prismatic crystal belonged to the triclinic space group P1, with unit-cell parameters a = 44.04, b = 45.11, c = 48.90,Å, , = 77.81, , = 87.34, , = 68.79°. Diffraction data were collected to 1.6,Å resolution. [source]

Hypotheses for the origin and early evolution of triterpenoid cyclases

GEOBIOLOGY, Issue 1 2007
W. 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]