Search results for "molecular clock"
showing 10 items of 54 documents
Molecular evolution of the arthropod hemocyanin superfamily.
2001
Arthropod hemocyanins are members of a protein superfamily that also comprises the arthropod phenoloxidases (tyrosinases), crustacean pseudohemocyanins (cryptocyanins), and insect storage hexamerins. The evolution of these proteins was inferred by neighbor-joining, maximum-parsimony, and maximum-likelihood methods. Monte Carlo shuffling approaches provided evidence against a discernible relationship of the arthropod hemocyanin superfamily and molluscan hemocyanins or nonarthropodan tyrosinases. Within the arthropod hemocyanin superfamily, the phenoloxidase probably emerged early in the (eu-)arthropod stemline and thus form the most likely outgroup. The respiratory hemocyanins evolved from t…
Monte Carlo simulation in phylogenies: an application to test the constancy of evolutionary rates.
1994
Monte Carlo simulation has commonly been used in phylogenetic studies to test different tree-reconstruction methods, and consequently, its application for testing evolutionary models can be considered as a natural extension of this usage. Repetitive simulation of a given evolutionary process, under the restrictions imposed by the model to be tested, along a determinate tree topology allow the estimate of probability distributions for the desired parameters. Next, the phylogenetic tree can be reconstructed again without the constraints of the model, and the parameter of interest, derived from this tree, can be compared to the corresponding probability distribution derived from the restricted…
Molecular phylogeny of the Notostraca
2012
Abstract We used a combined analysis of one nuclear (28S rDNA) and three mitochondrial markers (COI, 12S rDNA, 16S rDNA) to infer the molecular phylogeny of the Notostraca, represented by samples from the six continents that are inhabited by this group of branchiopod crustaceans. Our results confirm the monophyly of both extant notostracan genera Triops and Lepidurus with good support in model based and maximum parsimony analyses. We used branchiopod fossils as a calibration to infer divergence times among notostracan lineages and accounted for rate heterogeneity among lineages by applying relaxed-clock models. Our divergence date estimates indicate an initial diversification into the gener…
Ancient or recent? Insights into the temporal evolution of the Bruniaceae
2008
AbstractThe Bruniaceae are a South African plant family endemic to the Cape Floristic Region with one geographic outlier (Raspalia trigyna) in the Natal Province. Recent molecular phylogenetic analyses have cast new light upon inter- and intra-generic relationships within the family. The present work uses those data to gain insights into the temporal evolution of Bruniaceae by inferring a molecular clock. For calibration, the inferred age of Berzelia cordifolia (3–5My) was used, based on its distribution restricted to the geologically young limestone area around Bredasdorp. The results are consistent with the purported Cretaceous age of the family (‘palaeoendemics’), but also suggest that m…
Repeat intercontinental dispersal and Pleistocene speciation in disjunct Mediterranean and desert Senecio (Asteraceae).
2003
To explore the biogeographic history of Mediterranean/arid plant disjunctions, Old and New World Senecio sect. Senecio were analyzed phylogenetically using nuclear ribosomal DNA sequences (ITS). A clade corresponding to sect. Senecio was strongly supported. Area optimization indicated this clade to be of southern African origin. The Mediterranean and southern African floras were not distinguishable as sources of the main New World lineage, estimated to have become established during the middle Pliocene. Another previously suspected recent dispersal to the New World from the Mediterranean was confirmed for the recently recognized disjunction in S. mohavensis. The loss of suitable land connec…
Origin and phylogeography of the Chagas disease main vector Triatoma infestans based on nuclear rDNA sequences and genome size
2004
For about half of all Chagas disease cases T. infestans has been the responsible vector. Contributing to its genetic knowledge will increase Our understanding of the capacity of geographic expansion and domiciliation of triatomines. Populations of all infestans subcomplex species, T. infestans, T. delpontei, T. platensis and T. melanosoma and the so-called T. infestans "dark morph", from many South American countries were studied. A total of 10 and 7 different ITS-2 and ITS-1 haplotypes, respectively, were found. The total intraspecific ITS-2 nucleotide variability detected in T. infestans is the highest hitherto known in triatomines. ITS-1 minisatellites, detected for the first time in tri…
Nuclear rDNA-based molecular clock of the evolution of Triatominae (Hemiptera : Reduviidae), vectors of Chagas disease
2000
The evolutionary history and times of divergence of triatomine bug lineages are estimated from molecular clocks inferred from nucleotide sequences of the small subunit SSU (18S) and the second internal transcribed spacer (ITS-2) of the nuclear ribosomal DNA of these reduviids. The 18S rDNA molecular clock rate in Triatominae, and Prosorrhynchan Hemiptera in general, appears to be of 1.8% per 100 million years (my). The ITS-2 molecular clock rate in Triatominae is estimated to be around 0.4-1% per 1 my, indicating that ITS-2 evolves 23-55 times faster than 18S rDNA. Inferred chronological data about the evolution of Triatominae fit well with current hypotheses on their evolutionary histories…
Nuclear rDNA pseudogenes in Chagas disease vectors: Evolutionary implications of a new 5.8S+ITS-2 paralogous sequence marker in triatomines of North,…
2013
A pseudogene, paralogous to rDNA 5.8S and ITS-2, is described in Meccus dimidiata dimidiata, M. d. capitata, M. d. maculippenis, M. d. hegneri, M. sp. aff. dimidiata, M. p. phyllosoma, M. p. longipennis, M. p. pallidipennis, M. p. picturata, M. p. mazzottii, Triatoma mexicana, Triatoma nitida and Triatoma sanguisuga, covering North America, Central America and northern South America. Such a nuclear rDNA pseudogene is very rare. In the 5.8S gene, criteria for pseudogene identification included length variability, lower GC content, mutations regarding the functional uniform sequence, and relatively high base substitutions in evolutionary conserved sites. At ITS-2 level, criteria were the shor…
A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes
2013
Summary Background Recent analyses of de novo DNA mutations in modern humans have suggested a nuclear substitution rate that is approximately half that of previous estimates based on fossil calibration. This result has led to suggestions that major events in human evolution occurred far earlier than previously thought. Results Here, we use mitochondrial genome sequences from ten securely dated ancient modern humans spanning 40,000 years as calibration points for the mitochondrial clock, thus yielding a direct estimate of the mitochondrial substitution rate. Our clock yields mitochondrial divergence times that are in agreement with earlier estimates based on calibration points derived from e…
Molecular phylogeny of the harvestmen genus Sabacon (Arachnida: Opiliones: Dyspnoi) reveals multiple Eocene–Oligocene intercontinental dispersal even…
2012
Abstract We investigated the phylogeny and biogeographic history of the Holarctic harvestmen genus Sabacon , which shows an intercontinental disjunct distribution and is presumed to be a relatively old taxon. Molecular phylogenetic relationships of Sabacon were estimated using multiple gene regions and Bayesian inference for a comprehensive Sabacon sample. Molecular clock analyses, using relaxed clock models implemented in BEAST, are applied to date divergence events. Biogeographic scenarios utilizing S-DIVA and Lagrange C++ are reconstructed over sets of Bayesian trees, allowing for the incorporation of phylogenetic uncertainty and quantification of alternative reconstructions over time. F…