Search results for "molecular clock"
showing 10 items of 54 documents
Climatic oscillations triggered post-Messinian speciation of Western Palearctic brown frogs (Amphibia, Anura, Ranidae)
2003
Abstract Oscillating glacial cycles over the past 2.4 million years are proposed to have had a major impact on the diversity of contemporary species communities. We used mitochondrial and nuclear DNA sequence data to infer phylogenetic relationships within Western Palearctic brown frogs and to test the influence of Pliocene and Pleistocene climatic changes on their evolution. We sequenced 1976 bp of the mitochondrial genes 16S rRNA and cytochrome b and of the nuclear rhodopsin gene for all current species and subspecies. Based on an established allozyme clock for Western Palearctic water frogs and substitution rate constancy among water frogs and brown frogs, we calibrated a molecular clock…
From Europe to Africa and vice versa: evidence for multiple intercontinental dispersal in ribbed salamanders (Genus Pleurodeles)
2004
Aim The intricate puzzle-like geography of the western Mediterranean is a product of long-term tectonic and orogenic events, supplemented by repeated climatic oscillations since the Pliocene. It offers numerous vicariance events that may be invoked to explain speciation in amphibians. We test for plausibility of two mutually exclusive Iberian–African vicariance hypotheses to explain the basal split within newts of the genus Pleurodeles: (1) the disconnection of the Betic arch c. 14 Ma and (2) the end of the Messinian salinity crisis 5.33 Ma. Location Specimens of P. waltl and P. poireti were sampled from 32 populations in Portugal, Spain, Morocco, Algeria and Tunisia. Methods Parts of th…
Analysis of the Overdispersed Clock in the Short-Term Evolution of Hepatitis C Virus: Using the E1/E2 Gene Sequences to Infer Infection Dates in a Si…
2006
Abstract The assumption of a molecular clock for dating events from sequence information is often frustrated by the presence of heterogeneity among evolutionary rates due, among other factors, to positively selected sites. In this work, our goal is to explore methods to estimate infection dates from sequence analysis. One such method, based on site stripping for clock detection, was proposed to unravel the clocklike molecular evolution in sequences showing high variability of evolutionary rates and in the presence of positive selection. Other alternatives imply accommodating heterogeneity in evolutionary rates at various levels, without eliminating any information from the data. Here we pre…
Quaternary diversification in European alpine plants: pattern and process
2004
Molecular clock approaches applied previously to European alpine plants suggest that Primula sect. Auricula , Gentiana sect. Ciminalis and Soldanella diversified at the beginning of the Quaternary or well within this period, whereas Globularia had already started diversifying in the (Late–)Tertiary. In the first part of this paper we present evidence that, in contrast to Globularia and Soldanella , the branching patterns of the molecular internal transcribed spacer phylogenies of both Primula and Gentiana are incompatible with a constant–rates birth–death model. In both of these last two taxa, speciation probably decreased through Quaternary times, perhaps because of some niche–filling pro…
Phylogenetic analysis of the isopenicillin-N-synthetase horizontal gene transfer.
1996
A phylogenetic study of the isopenicillin-N-synthetase (IPNS) gene sequence from prokaryotic and lower eukaryotic producers of beta-lactam antibiotics by means of a maximum-likelihood approach has been carried out. After performing an extensive search, rather than invoking a global molecular clock, the results obtained are best explained by a model with three rates of evolution. Grouped in decreasing order, these correspond to A. nidulans and then to the rest of the eukaryotes and prokaryotes, respectively. The estimated branching date between prokaryotic and fungal IPNS sequences (852 +/- 106 MY) strongly supports the hypothesis that the IPNS gene was horizontally transferred from bacteria…
The diversity and evolution of chelicerate hemocyanins
2012
Abstract Background Oxygen transport in the hemolymph of many arthropod species is facilitated by large copper-proteins referred to as hemocyanins. Arthropod hemocyanins are hexamers or oligomers of hexamers, which are characterized by a high O2 transport capacity and a high cooperativity, thereby enhancing O2 supply. Hemocyanin subunit sequences had been available from horseshoe crabs (Xiphosura) and various spiders (Araneae), but not from any other chelicerate taxon. To trace the evolution of hemocyanins and the emergence of the large hemocyanin oligomers, hemocyanin cDNA sequences were obtained from representatives of selected chelicerate classes. Results Hemocyanin subunits from a sea s…
Constraining the Deep Origin of Parasitic Flatworms and Host-Interactions with Fossil Evidence
2015
Novel fossil discoveries have contributed to our understanding of the evolutionary appearance of parasitism in flatworms. Furthermore, genetic analyses with greater coverage have shifted our views on the coevolution of parasitic flatworms and their hosts. The putative record of parasitic flatworms is consistent with extant host associations and so can be used to put constraints on the evolutionary origin of the parasites themselves. The future lies in new molecular clock analyses combined with additional discoveries of exceptionally preserved flatworms associated with hosts and coprolites. Besides direct evidence, the host fossil record and biogeography have the potential to constrain their…
Sister species within the Triops cancriformis lineage (Crustacea, Notostraca)
2006
301 Korn, M., Marrone, F., Perez-Bote, J. L., Machado, M., Cristo, M., Cancela da Fonseca, L. & Hundsdoerfer, A. K. (2006). Sister species within the Triops cancriformis lineage (Crustacea, Notostraca). — Zoologica Scripta , 35 , 301–322. We investigated the phylogenetic relationships among the three presently recognized subspecies of the tadpole shrimp, Triops cancriformis , using mitochondrial 16S and 12S rDNA sequences. Our results indicate that the taxon is divided into two distinct lineages. One lineage is formed of T. c. cancriformis populations and samples from northern Spain that had been classified as T. c. simplex in the most recent literature. The second lineage comprises all pop…
The phylogeny and biogeography of Gentiana L. sect. Ciminalis (Adans.) Dumort.: A historical interpretation of distribution ranges in the European hi…
1998
Abstract Gentiana sect. Ciminalis consists of seven mostly ecologically or geographically vicariant and closely related species which are distributed throughout the South and Central European high mountains. The analysis of a RAPD data set and trn L-intron and ITS sequences resulted in slightly different phylogenetic hypotheses. In the preferred hypothesis the group consists of two completely resolved main lineages: 1) G. clusii and G. alpina. 2) G. dinarica, G. acaulis, G. ligustica, G. angustifolia and G. occidentalis. The most important conclusions we have drawn from this phylogenetic hypothesis and from the observed patterns of molecular variation are: 1) The calcifuge ecology of G. aca…
Unique clockwork in photoreceptor of rat
2010
In mammals, the retina contains a clock system that oscillates independently of the master clock in the suprachiasmatic nucleus and allows the retina to anticipate and to adapt to the sustained daily changes in ambient illumination. Using a combination of laser capture micro-dissection and quantitative PCR in the present study, the clockwork of mammalian photoreceptors has been recorded. The transcript amounts of the core clock genes Clock, Bmal1, Period1 (Per1), Per3, Cryptochrome2, and Casein kinase Ie in photoreceptors of rat retina have been found to undergo daily changes. Clock and Bmal1 peak with Per1 and Per3 around dark onset, whereas Casein kinase Ie and Cryptochrome2 peak at night…