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Search Results: 1 - 10 of 8334 matches for " Molecular dating "
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A revised dated phylogeny of the arachnid order Opiliones
Prashant P. Sharma,Gonzalo Giribet
Frontiers in Genetics , 2014, DOI: 10.3389/fgene.2014.00255
Abstract: Dating the Opiliones tree of life has become an important enterprise for this group of arthropods, due to their ancient origins and important biogeographic implications. To incorporate both methodological innovations in molecular dating as well as new systematic discoveries of harvestman diversity, we conducted total evidence dating on a data set uniting morphological and/or molecular sequence data for 47 Opiliones species, including all four well-known Palaeozoic fossils, to test the placement of both fossils and newly discovered lineages in a single analysis. Furthermore, we investigated node dating with a phylogenomic data set of 24,202 amino acid sites for 14 species of Opiliones, sampling all extant suborders. In this way, we approached molecular dating of basal harvestman phylogeny using different data sets and approaches to assess congruence of divergence time estimates. In spite of the markedly different composition of data sets, our results show congruence across all analyses for age estimates of basal nodes that are well constrained with respect to fossil calibrations (e.g., Opiliones, Palpatores). By contrast, derived nodes that lack fossil calibrations (e.g., the suborders Cyphophthalmi, and Laniatores) have large uncertainty intervals in diversification times, particularly in the total evidence dating analysis, reflecting the dearth of calibration points and undersampling of derived lineages. Total evidence dating consistently produced older median ages than node dating for ingroup nodes, due to the nested placement of multiple Palaeozoic fossils. Our analyses support basal diversification of Opiliones in the Ordovician-Devonian period, corroborating the inferred ancient origins of this arthropod order, and underscore the importance of diversity discovery—both paleontological and neontological—in evolutionary inference.
Extensive remodeling of the Pseudomonas syringae pv. avellanae type III secretome associated with two independent host shifts onto hazelnut
Heath E O'Brien, Shalabh Thakur, Yunchen Gong, Pauline Fung, Jianfeng Zhang, Lijie Yuan, Pauline W Wang, Choseung Yong, Marco Scortichini, David S Guttman
BMC Microbiology , 2012, DOI: 10.1186/1471-2180-12-141
Abstract: We found little evidence for horizontal transfer (recombination) of genes between Pav lineages, but two large genomic islands (GIs) have been recently acquired by one of the lineages. Evolutionary analyses of the genes encoding type III secreted effectors (T3SEs) that are translocated into host cells and are important for both suppressing and eliciting defense responses show that the two Pav lineages have dramatically different T3SE profiles, with only two shared putatively functional T3SEs. One Pav lineage has undergone unprecedented secretome remodeling, including the acquisition of eleven new T3SEs and the loss or pseudogenization of 15, including five of the six core T3SE families that are present in the other Pav lineage. Molecular dating indicates that divergence within both of the Pav lineages predates their observation in the field. This suggest that both Pav lineages have been cryptically infecting hazelnut trees or wild relatives for many years, and that the emergence of hazelnut decline in the 1970s may have been due to changes in agricultural practice.These data show that divergent lineages of P. syringae can converge on identical disease etiology on the same host plant using different virulence mechanisms and that dramatic shifts in the arsenal of T3SEs can accompany disease emergence.
Cyprinid phylogeny based on Bayesian and maximum likelihood analyses of partitioned data: implications for Cyprinidae systematics
XuZhen Wang,XiaoNi Gan,JunBing Li,Richard L. Mayden,ShunPing He
Science China Life Sciences , 2012, DOI: 10.1007/s11427-012-4366-z
Abstract: Cyprinidae is the biggest family of freshwater fish, but the phylogenetic relationships among its higher-level taxa are not yet fully resolved. In this study, we used the nuclear recombination activating gene 2 and the mitochondrial 16S ribosomal RNA and cytochrome b genes to reconstruct cyprinid phylogeny. Our aims were to (i) demonstrate the effects of partitioned phylogenetic analyses on phylogeny reconstruction of cyprinid fishes; (ii) provide new insights into the phylogeny of cyprinids. Our study indicated that unpartitioned strategy was optimal for our analyses; partitioned analyses did not provide better-resolved or -supported estimates of cyprinid phylogeny. Bayesian analyses support the following relationships among the major monophyletic groups within Cyprinidae: (Cyprininae, Labeoninae), ((Acheilognathinae, ((Leuciscinae, Tincinae), Gobioninae)), Xenocyprininae). The placement of Danioninae was poorly resolved. Estimates of divergence dates within the family showed that radiation of the major cyprinid groups occurred during the Late Oligocene through the Late Miocene. Our phylogenetic analyses improved our understanding of the evolutionary history of this important fish family.
Mitochondrial genome sequences reveal deep divergences among Anopheles punctulatus sibling species in Papua New Guinea
Logue Kyle,Chan Ernest R,Phipps Tenisha,Small Scott T
Malaria Journal , 2013, DOI: 10.1186/1475-2875-12-64
Abstract: Background Members of the Anopheles punctulatus group (AP group) are the primary vectors of human malaria in Papua New Guinea. The AP group includes 13 sibling species, most of them morphologically indistinguishable. Understanding why only certain species are able to transmit malaria requires a better comprehension of their evolutionary history. In particular, understanding relationships and divergence times among Anopheles species may enable assessing how malaria-related traits (e.g. blood feeding behaviours, vector competence) have evolved. Methods DNA sequences of 14 mitochondrial (mt) genomes from five AP sibling species and two species of the Anopheles dirus complex of Southeast Asia were sequenced. DNA sequences from all concatenated protein coding genes (10,770 bp) were then analysed using a Bayesian approach to reconstruct phylogenetic relationships and date the divergence of the AP sibling species. Results Phylogenetic reconstruction using the concatenated DNA sequence of all mitochondrial protein coding genes indicates that the ancestors of the AP group arrived in Papua New Guinea 25 to 54 million years ago and rapidly diverged to form the current sibling species. Conclusion Through evaluation of newly described mt genome sequences, this study has revealed a divergence among members of the AP group in Papua New Guinea that would significantly predate the arrival of humans in this region, 50 thousand years ago. The divergence observed among the mtDNA sequences studied here may have resulted from reproductive isolation during historical changes in sea-level through glacial minima and maxima. This leads to a hypothesis that the AP sibling species have evolved independently for potentially thousands of generations. This suggests that the evolution of many phenotypes, such as insecticide resistance will arise independently in each of the AP sibling species studied here.
A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes
Diana Chernikova, Sam Motamedi, Miklós Csür?s, Eugene V Koonin, Igor B Rogozin
Biology Direct , 2011, DOI: 10.1186/1745-6150-6-26
Abstract: We applied the genome-wide analysis of rare genomic changes associated with conserved amino acids (RGC_CAs) and used several independent techniques to obtain date estimates for the divergence of the major lineages of eukaryotes with calibration intervals for insects, land plants and vertebrates. The results suggest an early divergence of monocot and dicot plants, approximately 340 Mya, raising the possibility of plant-insect coevolution. The divergence of bilaterian animal phyla is estimated at ~400-700 Mya, a range of dates that is consistent with cladogenesis immediately preceding the Cambrian explosion. The origin of opisthokonts (the supergroup of eukaryotes that includes metazoa and fungi) is estimated at ~700-1,000 Mya, and the age of LECA at ~1,000-1,300 Mya. We separately analyzed the red algal calibration interval which is based on single fossil. This analysis produced time estimates that were systematically older compared to the other estimates. Nevertheless, the majority of the estimates for the age of the LECA using the red algal data fell within the 1,200-1,400 Mya interval.The inference of a "young LECA" is compatible with the latest of previously estimated dates and has substantial biological implications. If these estimates are valid, the approximately 1 to 1.4 billion years of evolution of eukaryotes that is open to comparative-genomic study probably was preceded by hundreds of millions years of evolution that might have included extinct diversity inaccessible to comparative approaches.This article was reviewed by William Martin, Herve Philippe (nominated by I. King Jordan), and Romain Derelle.Estimation of divergence dates for biological taxa from molecular data is a perilous exercise fraught by artifacts which become progressively more severe for events further in the past [1,2]. There are many factors that hamper molecular time estimates, especially for ancient events. Some of the most important problems are violations of the molecular clock, unc
Tectonic calibrations in molecular dating
Current Zoology , 2011,
Abstract: Molecular dating techniques require the use of calibrations, which are usually fossil or geological vicariance-based. Fossil calibrations have been criticised because they result only in minimum age estimates. Based on a historical biogeographic perspective, I suggest that vicariance-based calibrations are more dangerous. Almost all analytical methods in historical biogeography are strongly biased towards inferring vicariance, hence vicariance identified through such methods is unreliable. Other studies, especially of groups found on Gondwanan fragments, have simply assumed vicariance. Although it was previously believed that vicariance was the predominant mode of speciation, mounting evidence now indicates that speciation by dispersal is common, dominating vicariance in several groups. Moreover, the possibility of speciation having occurred before the said geological event cannot be precluded. Thus, geological calibrations can under- or overestimate times, whereas fossil calibrations always result in minimum estimates. Another major drawback of vicariant calibrations is the problem of circular reasoning when the resulting estimates are used to infer ages of biogeographic events. I argue that fossil-based dating is a superior alternative to vicariance, primarily because the strongest assumption in the latter, that speciation was caused by the said geological process, is more often than not the most tenuous. When authors prefer to use a combination of fossil and vicariant calibrations, one suggestion is to report results both with and without inclusion of the geological constraints. Relying solely on vicariant calibrations should be strictly avoided [Current Zoology 57 (1): 116–124, 2011].
Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans
Frédéric Delsuc, Sergio F Vizcaíno, Emmanuel JP Douzery
BMC Evolutionary Biology , 2004, DOI: 10.1186/1471-2148-4-11
Abstract: We applied a Bayesian approach to three nuclear genes in order to relax the molecular clock assumption while accounting for differences in evolutionary dynamics among genes and incorporating paleontological uncertainties. We obtained a molecular time scale for the evolution of extant xenarthrans and other placental mammals. Divergence time estimates provide substantial evidence for contemporaneous diversification events among independent xenarthran lineages. This correlated pattern of diversification might possibly relate to major environmental changes that occurred in South America during the Cenozoic.The observed synchronicity between planetary and biological events suggests that global change played a crucial role in shaping the evolutionary history of extant xenarthrans. Our findings open ways to test this hypothesis further in other South American mammalian endemics like hystricognath rodents, platyrrhine primates, and didelphid marsupials.Paleobiological studies aim at assessing the influence of past environmental changes on the evolutionary history of organisms. To be reliable these macroevolutionary studies must consider groups possessing a high quality fossil record coupled with a well documented history of past environmental changes encompassing geological, ecological, climatic and biogeographical events [1]. Inferring the impact of these historical events on the evolution of faunas is particularly difficult in cases where dispersal occurred repeatedly between biogeographic areas. For this reason, islands have for long attracted particular interest by acting as natural laboratories for the study of evolution [2]. Owing to its "splendid isolation" from other continental land masses for a great part of the Tertiary era [3], South America offers a special case of continental island-like evolution with its very peculiar mammalian fauna composed of an initial nucleus of autochthonous taxa subsequently enriched by few successive waves of successful immigrants.Nu
The origin of modern frogs (Neobatrachia) was accompanied by acceleration in mitochondrial and nuclear substitution rates
Irisarri Iker,Mauro Diego San,Abascal Federico,Ohler Annemarie
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-626
Abstract: Background Understanding the causes underlying heterogeneity of molecular evolutionary rates among lineages is a long-standing and central question in evolutionary biology. Although several earlier studies showed that modern frogs (Neobatrachia) experienced an acceleration of mitochondrial gene substitution rates compared to non-neobatrachian relatives, no further characterization of this phenomenon was attempted. To gain new insights on this topic, we sequenced the complete mitochondrial genomes and nine nuclear loci of one pelobatoid (Pelodytes punctatus) and five neobatrachians, Heleophryne regis (Heleophrynidae), Lechriodus melanopyga (Limnodynastidae), Calyptocephalella gayi (Calyptocephalellidae), Telmatobius bolivianus (Ceratophryidae), and Sooglossus thomasseti (Sooglossidae). These represent major clades not included in previous mitogenomic analyses, and most of them are remarkably species-poor compared to other neobatrachians. Results We reconstructed a fully resolved and robust phylogeny of extant frogs based on the new mitochondrial and nuclear sequence data, and dated major cladogenetic events. The reconstructed tree recovered Heleophryne as sister group to all other neobatrachians, the Australasian Lechriodus and the South American Calyptocephalella formed a clade that was the sister group to Nobleobatrachia, and the Seychellois Sooglossus was recovered as the sister group of Ranoides. We used relative-rate tests and direct comparison of branch lengths from mitochondrial and nuclear-based trees to demonstrate that both mitochondrial and nuclear evolutionary rates are significantly higher in all neobatrachians compared to their non-neobatrachian relatives, and that such rate acceleration started at the origin of Neobatrachia. Conclusions Through the analysis of the selection coefficient (ω) in different branches of the tree, we found compelling evidence of relaxation of purifying selection in neobatrachians, which could (at least in part) explain the observed higher mitochondrial and nuclear substitution rates in this clade. Our analyses allowed us to discard that changes in substitution rates could be correlated with increased mitochondrial genome rearrangement or diversification rates observed in different lineages of neobatrachians.
Electron spin resonance dating of shells from the sambaqui (shell mound) Capelinha, S?o Paulo, Brazil
Kinoshita, A.;Figuty, L.;Baffa, O.;
Brazilian Journal of Physics , 2006, DOI: 10.1590/S0103-97332006000100016
Abstract: capelinha is a fluvial sambaqui (brazilian shell mound) located in the ribeira valey in the state of s?o paulo that is being studied. it is one of the oldest sambaquis located along a river dated so far in this region. the use of esr to date other shells stimulated our group to apply this method to the capelinha site. shells from land snails (megalobulimus sp.) obtained in two levels of excavations were analyzed; one of them was in contact with a skeleton that was dated by c-14. the archeological doses obtained were (8.05±0.07) gy and (9.50±0.03) gy. since the last site was previously dated by c-14 (beta -analytics, beta 153988) giving: 8860 +/- 60 years bp (conventional age) and 10180 to 9710 years bp (calibrated age), the archeological dose found for this shell was used to determine the local rate of (0.93 to 0.98) mgy/year, that aggress with other surveys done in the region. using this dose rate the age of the second shell was found to be 8.14 to 8.73 ky bp that agrees with the stratigraphy of the site.
Electron spin resonance dating of shells from the sambaqui (shell mound) Capelinha, S o Paulo, Brazil
Kinoshita A.,Figuty L.,Baffa O.
Brazilian Journal of Physics , 2006,
Abstract: Capelinha is a fluvial sambaqui (Brazilian Shell Mound) located in the Ribeira Valey in the State of S o Paulo that is being studied. It is one of the oldest sambaquis located along a river dated so far in this region. The use of ESR to date other shells stimulated our group to apply this method to the Capelinha site. Shells from land snails (Megalobulimus sp.) obtained in two levels of excavations were analyzed; one of them was in contact with a skeleton that was dated by C-14. The archeological doses obtained were (8.05±0.07) Gy and (9.50±0.03) Gy. Since the last site was previously dated by C-14 (Beta -Analytics, Beta 153988) giving: 8860 +/- 60 years BP (conventional age) and 10180 to 9710 years BP (calibrated age), the archeological dose found for this shell was used to determine the local rate of (0.93 to 0.98) mGy/year, that aggress with other surveys done in the region. Using this dose rate the age of the second shell was found to be 8.14 to 8.73 ky BP that agrees with the stratigraphy of the site.
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