Evidence for local DNA influences on patterns of substitutions in the human α-interferon gene family

1986 ◽  
Vol 28 (4) ◽  
pp. 483-496 ◽  
Author(s):  
G. Brian Golding ◽  
Barry W. Glickman
Keyword(s):  
Dna Sequences ◽  
Evolutionary History ◽  
Spontaneous Mutation ◽  
Direct Repeat ◽  
Base Substitution ◽  
Human Interferon ◽  
Parsimony Method ◽  
Maximum Parsimony Method ◽  
Ancestral Sequences ◽  
History Of

The evolutionary history of genes can be used to examine patterns of spontaneous mutation if the sequences are sufficiently extensive to provide reliable data. Many human α-interferon genes have been sequenced and they form a large multigene family including several pseudogenes. A phylogenetic history for 15 human interferon sequences was reconstructed and their ancestral sequences inferred using a maximum parsimony method. This evolutionary history provided a record of more than 738 spontaneous mutations that have occurred in man's recent evolution. Of these mutations, more than 267 base substitution and deletion–insertion events were analyzed to determine the possible effects of nearby DNA sequences. Many substitutions occur at the end of long runs of identical bases and some dinucleotide pairs may mutate more often than others. Because templating by local DNA sequences has been implicated in prokaryotic mutation, the sequences were also examined for nearby repeats that include the substituted nucleotide and hence are potentially capable of templating the substitution. The majority of sequence alterations examined have either a similar direct repeat or palindrome nearby. Often such templates can account for simultaneous multiple mutations. These results suggest that sequence-directed events may occur occasionally in eukaryotes and that neighbouring DNA sequences can influence both the occurrence and types of mutations in several different ways.Key words: spontaneous mutation, template-directed mutations, phylogenetic history, evolution.

scholarly journals A rapid loss of stripes: the evolutionary history of the extinct quagga

2005 ◽  
Vol 1 (3) ◽  
pp. 291-295 ◽  
Author(s):  
Jennifer A Leonard ◽  
Nadin Rohland ◽  
Scott Glaberman ◽  
Robert C Fleischer ◽  
Adalgisa Caccone ◽  
...  
Keyword(s):  
South African ◽  
Dna Sequences ◽  
Evolutionary History ◽  
Climate Changes ◽  
Rapid Loss ◽  
Mt Dna ◽  
Pleistocene Climate ◽  
Equus Burchelli ◽  
History Of ◽  
Plains Zebra

Twenty years ago, the field of ancient DNA was launched with the publication of two short mitochondrial (mt) DNA sequences from a single quagga ( Equus quagga ) museum skin, an extinct South African equid ( Higuchi et al . 1984 Nature 312 , 282–284). This was the first extinct species from which genetic information was retrieved. The DNA sequences of the quagga showed that it was more closely related to zebras than to horses. However, quagga evolutionary history is far from clear. We have isolated DNA from eight quaggas and a plains zebra (subspecies or phenotype Equus burchelli burchelli ). We show that the quagga displayed little genetic diversity and very recently diverged from the plains zebra, probably during the penultimate glacial maximum. This emphasizes the importance of Pleistocene climate changes for phylogeographic patterns in African as well as Holarctic fauna.

scholarly journals Evolutionary Relationship between Two Firefly Species,Curtos costipennisandC. okinawanus(Coleoptera, Lampyridae), in the Ryukyu Islands of Japan Revealed by the Mitochondrial and Nuclear DNA Sequences

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Masahiko Muraji ◽  
Norio Arakaki ◽  
Shigeo Tanizaki
Keyword(s):  
Dna Sequences ◽  
Evolutionary History ◽  
Nuclear Dna ◽  
Evolutionary Relationship ◽  
Early Pleistocene ◽  
Ryukyu Islands ◽  
Mtdna Sequences ◽  
Northern Half ◽  
The Ryukyu Islands ◽  
History Of

The phylogenetic relationship, biogeography, and evolutionary history of closely related two firefly species,Curtos costipennisandC. okinawanus, distributed in the Ryukyu Islands of Japan were examined based on nucleotide sequences of mitochondrial (2.2 kb long) and nuclear (1.1-1.2 kb long) DNAs. In these analyses, individuals were divided among three genetically distinct local groups,C. costipennisin the Amami region,C. okinawanusin the Okinawa region, andC. costipennisin the Sakishima region. Their mtDNA sequences suggested that ancestralC. costipennispopulation was first separated between the Central and Southern Ryukyu areas, and the northern half was then subdivided betweenC. costipennisin the Amami andC. okinawanusin the Okinawa. The application of the molecular evolutionary clocks of coleopteran insects indicated that their vicariance occurred 1.0–1.4 million years ago, suggesting the influence of submergence and subdivision of a paleopeninsula extending between the Ryukyu Islands and continental China through Taiwan in the early Pleistocene.

scholarly journals Intraspecific Phylogeography and Adaptive Divergence in the White-Headed Woodpecker

The Condor ◽  
2006 ◽  
Vol 108 (3) ◽  
pp. 489-508
Author(s):  
Matthew P. Alexander ◽  
Kevin J. Burns
Keyword(s):  
Evolutionary History ◽  
Base Substitution ◽  
Adaptive Divergence ◽  
Restricted Gene Flow ◽  
Phylogeographic Analysis ◽  
Transverse Ranges ◽  
Phylogeographic History ◽  
History Of ◽  
Pinus Coulteri ◽  
Intraspecific Phylogeography

AbstractThis study uses mitochondrial DNA (mtDNA) to examine the phylogeography of the White-headed Woodpecker (Picoides albolarvatus), one of the least-studied woodpeckers in North America. A mismatch distribution and calculation of Tajima's D indicate that the overall phylogeographic history of the species is characterized by a recent range expansion that probably occurred after the start of the Pleistocene. In addition, a nested clade phylogeographic analysis indicates that additional processes such as allopatric fragmentation and restricted gene flow have influenced the evolutionary history of this species. Traditionally, the White-headed Woodpecker has been split into two subspecies whose distributions meet in the northern part of the Transverse Ranges in California. The two subspecies differ morphologically, with the southern subspecies having a larger bill in proportion to its body size than the northern subspecies. Geographical variation in mtDNA is concordant with a division at the Transverse Ranges that corresponds to the morphological variation seen between the two subspecies. An analysis of molecular variance indicates that 27% of the genetic variation results from differences between the northern and southern subspecies. Furthermore, birds in the northern part of the range differ from those in the southern part of the range by at least one base substitution. These results agree with the hypothesis that the larger bill of the southern subspecies is the result of recent local adaptation to feeding on the large cones of Coulter pines (Pinus coulteri).

Phylogenetic studies of Saprolegniomycetidae and related groups based on nuclear large subunit ribosomal DNA sequences

2000 ◽  
Vol 77 (12) ◽  
pp. 1790-1800 ◽  
Author(s):  
Alexandra Riethmüller ◽  
Michael Weiß ◽  
Franz Oberwinkler
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Bootstrap Method ◽  
Large Subunit ◽  
Phytophthora Megasperma ◽  
Parsimony Method ◽  
Natural Group ◽  
Maximum Parsimony Method ◽  
Phylogenetic Studies ◽  
Main Emphasis

To reveal phylogenetic relationships within the Peronosporomycetes (Oomycetes), we sequenced a part of the nuclear rDNA coding for the ribosomal large subunit of 46 Peronosporomycetes species and one representative of the Xanthophyta. The main emphasis of our study was put on the phylogenetic relationships within the Saprolegniomycetidae. We supplemented our data with a sequence of Phytophthora megasperma Drechsler from GenBank. Two sets of sequences were analysed using the neighbor-joining method, statistically supported by the bootstrap method, as well as the maximum parsimony method. Our results are well compatible with the tripartite subclassification of the Peronosporomycetes into Saprolegniomycetidae, Rhipidiomycetidae and Peronosporomycetidae, as well as with the placement of the orders Saprolegniales and Leptomitales in the Saprolegniomycetidae. Pachymetra chaunorhiza Croft & Dick, which has been placed in the Sclerosporales, was grouped within the Saprolegniales. Within the Peronosporomycetidae, the orders Peronosporales and Pythiales could not be separated. There are indications that Phytophthora de Bary and the Peronosporales form a common natural group. The genus Achlya Nees proved to be a heterogeneous group.

Karyotype Evolution and Distinct Evolutionary History of the W Chromosomes in Swallows (Aves, Passeriformes)

2019 ◽  
Vol 158 (2) ◽  
pp. 98-105 ◽  
Author(s):  
Suziane A. Barcellos ◽  
Rafael Kretschmer ◽  
Marcelo S. de Souza ◽  
Alice L. Costa ◽  
Tiago M. Degrandi ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Evolutionary History ◽  
Karyotype Evolution ◽  
Sex Chromosome ◽  
Repetitive Sequences ◽  
Z Chromosome ◽  
W Chromosome ◽  
The Family ◽  
Agnor Staining ◽  
History Of

As in many other bird groups, data on karyotype organization and distribution of repetitive sequences are also lacking in species belonging to the family Hirundinidae. Thus, in the present study, we analyzed the karyotypes of 3 swallow species (Progne tapera, Progne chalybea, and Pygochelidon cyanoleuca) by Giemsa and AgNOR staining, C-banding, and FISH with 11 microsatellite sequences. The diploid chromosome number was 2n = 76 in all 3 species, and NORs were observed in 2 chromosome pairs each. The microsatellite distribution pattern was similar in both Progne species, whereas P. cyanoleuca presented a distinct organization. These repetitive DNA sequences were found in the centromeric, pericentromeric, and telomeric regions of the macrochromosomes, as well as in 2 interstitial blocks in the W chromosome. Most microchromosomes had mainly telomeric signals. The Z chromosome displayed 1 hybridization signal in P. tapera but none in the other species. In contrast, the W chromosome showed an accumulation of different microsatellite sequences. The swallow W chromosome is larger than that of most Passeriformes. The observed enlargement in chromosome size might be explained by these high amounts of repetitive sequences. In sum, our data highlight the significant role that microsatellite sequences may play in sex chromosome differentiation.

scholarly journals Population Structure of Plasmid-Containing Strains of Streptococcus mutans, a Member of the Human Indigenous Biota

2006 ◽  
Vol 189 (4) ◽  
pp. 1238-1243 ◽  
Author(s):  
Page W. Caufield ◽  
Deepak Saxena ◽  
David Fitch ◽  
Yihong Li
Keyword(s):  
Streptococcus Mutans ◽  
Dna Sequences ◽  
Evolutionary History ◽  
Hypervariable Region ◽  
Intergenic Spacer ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Intergenic Spacer Region ◽  
Asian Clade ◽  
History Of

ABSTRACT There are suggestions that the phylogeny of Streptococcus mutans, a member of the human indigenous biota that is transmitted mostly mother to child, might parallel the evolutionary history of its human host. The relatedness and phylogeny of plasmid-containing strains of S. mutans were examined based on chromosomal DNA fingerprints (CDF), a hypervariable region (HVR) of a 5.6-kb plasmid, the rRNA gene intergenic spacer region (IGSR), serotypes, and the genotypes of mutacin I and II. Plasmid-containing strains were studied because their genetic diversity was twice as great as that of plasmid-free strains. The CDF of S. mutans from unrelated human hosts were unique, except those from Caucasians, which were essentially identical. The evolutionary history of the IGSR, with or without the serotype and mutacin characters, clearly delineated an Asian clade. Also, a continuous association with mutacin II could be reconstructed through an evolutionary lineage with the IGSR, but not for serotype e. DNA sequences from the HVR of the plasmid produced a well-resolved phylogeny that differed from the chromosomal phylogeny, indicating that the horizontal transfer of the plasmid may have occurred multiple times. The plasmid phylogeny was more congruent with serotype e than with mutacin II evolution, suggesting a possible functional correlation. Thus, the history of this three-tiered relationship between human, bacterium, and plasmid supported both coevolution and independent evolution.

scholarly journals Structural Changes and Adaptative Evolutionary Constraints In FLOWERING LOCUS T and TERMINAL FLOWER1-Like Genes of Flowering Plants

2021 ◽  
Author(s):  
Deivid Almeida de Jesus ◽  
Darlisson Mesquista Batista ◽  
Shayla Salzman ◽  
Lucas Miguel Carvalho ◽  
Kaue Santana ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Structural Changes ◽  
Protein Structures ◽  
Flowering Phenology ◽  
Flowering Locus T ◽  
Ancestral Sequences ◽  
Terminal Flower 1 ◽  
History Of ◽  
Flowering Locus ◽  
Complex Signaling

Abstract Regulation of flowering is a crucial event in the evolutionary history of angiosperms. The production of flowers is regulated through the integration of different environmental and endogenous stimuli, many of which involve the activation of different genes in a hierarchical and complex signaling network. The FLOWERING LOCUS T/TERMINAL FLOWER 1 (FT/TFL1) gene family is known to regulate important aspects of flowering in plants. To better understand the pivotal events that changed FT and TFL1 functions during the evolution of angiosperms, we reconstructed the ancestral sequences of FT/TFL1-like genes and predicted protein structures to identify determinant sites that evolved in both proteins and allowed the adaptative diversification in the flowering phenology and developmental processes. Residues from the P-loop domain of the analyzed FT structures showed predominantly high destabilizing mutations which is consistent with constant selective pressure found for this region. In addition, we demonstrate that the occurrence of destabilizing mutations in residues located at the phosphatidylcholine binding sites of FT structure experience positive selection, and some residues of 4th exon are under negative selection, which is compensated by the occurrence of stabilizing mutations in key regions and the P-loop to maintain the overall protein stability. Our results shed light on the evolutionary history of key genes involved in the diversification of angiosperms.

scholarly journals Evolutionary history of a relict conifer, Pseudotaxus chienii (Taxaceae), in south-east China during the late Neogene: old lineage, young populations

2019 ◽  
Vol 125 (1) ◽  
pp. 105-117 ◽  
Author(s):  
Yixuan Kou ◽  
Li Zhang ◽  
Dengmei Fan ◽  
Shanmei Cheng ◽  
Dezhu Li ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genetic Divergence ◽  
Evolutionary History ◽  
Isolation By Distance ◽  
Demographic History ◽  
East China ◽  
Population Divergence ◽  
Isolation By Environment ◽  
Late Neogene ◽  
History Of

Abstract Background and Aims Many monotypic gymnosperm lineages in south-east China paradoxically remain in relict status despite long evolutionary histories and ample opportunities for allopatric speciation, but this paradox has received little attention and has yet to be resolved. Here, we address this issue by investigating the evolutionary history of a relict conifer, Pseudotaxus chienii (Taxaceae). Methods DNA sequences from two chloroplast regions and 14 nuclear loci were obtained for 134 samples. The demographic history was inferred and the contribution of isolation by environment (IBE) in patterning genetic divergence was compared with that of isolation by distance (IBD). Key Results Three genetic clusters were identified. Approximate Bayesian computation analyses showed that the three clusters diverged in the late Pliocene (~3.68 Ma) and two admixture events were detected. Asymmetric gene flow and similar population divergence times (~ 3.74 Ma) were characterized using the isolation with migration model. Neither IBD nor IBE contributed significantly to genetic divergence, and the contribution of IBE was much smaller than that of IBD. Conclusions These results suggest that several monotypic relict gymnosperm lineages like P. chienii in south-east China did not remain in situ and undiversified for millions of years. On the contrary, they have been evolving and the extant populations have become established more recently, having insufficient time to speciate. Our findings provide a new perspective for understanding the formation and evolution of the relict gymnosperm flora of China as well as of the Sino-Japanese Flora.

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