共查询到20条相似文献,搜索用时 10 毫秒
1.
Moyle RG 《Evolution; international journal of organic evolution》2004,58(8):1871-1873
A recent molecular clock analysis concluded that Gondwanan vicariance and out-of-India dispersal best explained the distribution of Crypteroniaceae and its allies (Conti et al. 2002). A reanalysis of their data using a different molecular dating technique and calibration point is congruent with an alternative hypothesis, namely dispersal between India, Africa, and South America long after the initial break-up of Gondwana. 相似文献
2.
We have calibrated five different molecular clocks for circulating poliovirus based upon the rates of fixation of total substitutions (K(t)), synonymous substitutions (K(s)), synonymous transitions (A(s)), synonymous transversions (B(s)), and nonsynonymous substitutions (K(a)) into the P1/capsid region (2,643 nucleotides). Rates were determined over a 10-year period by analysis of sequences of 31 wild poliovirus type 1 isolates representing a well-defined phylogeny derived from a common imported ancestor. Similar rates were obtained by linear regression, the maximum likelihood/single-rate dated-tip method, and Bayesian inference. The very rapid K(t) [(1.03 +/- 0.10) x 10(-2) substitutions/site/year] and K(s) [(1.00 +/- 0.08) x 10(-2)] clocks were driven primarily by the A(s) clock [(0.96 +/- 0.09) x 10(-2)], the B(s) clock was approximately 10-fold slower [(0.10 +/- 0.03) x 10(-2)], and the more stochastic K(a) clock was approximately 30-fold slower [(0.03 +/- 0.01) x 10(-2)]. Nonsynonymous substitutions at all P1/capsid sites, including the neutralizing antigenic sites, appeared to be constrained by purifying selection. Simulation of the evolution of third-codon positions suggested that saturation of synonymous transitions would be evident at 10 years and complete at approximately 65 years of independent transmission. Saturation of synonymous transversions was predicted to be minimal at 20 years and incomplete at 100 years. The rapid evolution of the K(t), K(s), and A(s) clocks can be used to estimate the dates of divergence of closely related viruses, whereas the slower B(s) and K(a) clocks may be used to explore deeper evolutionary relationships within and across poliovirus genotypes. 相似文献
3.
Calibration of galliform molecular clocks using multiple fossils and genetic partitions 总被引:2,自引:0,他引:2
For more than a century, members of the traditional avian order Galliformes (i.e., pheasants, partridges, junglefowl, and relatives) have been among the most intensively studied birds, but still a comprehensive timeframe for their evolutionary history is lacking. Thanks to a number of recent cladistic interpretations for several galliform fossils, candidates now exist that can potentially be used as accurate internal calibrations for molecular clocks. Here, we describe a molecular timescale for Galliformes based on cytochrome b and ND2 using nine mostly internal fossil-based anchorpoints. Beyond application of calibrations spanning the entire evolutionary history of Galliformes, care was taken to investigate the effects of calibration choice, substitution saturation, and rate heterogeneity among lineages on divergence time estimation. Results show broad consistency in time estimation with five out of the nine total calibrations. Our divergence time estimates, based on these anchorpoints, indicate that the early history of Galliformes took place in the Cretaceous, including the origin of the basal-most megapode and perhaps cracid lineages, but that the remaining morphological diversification likely started in the earliest Tertiary. The multi-calibration/multi-genetic partition approach used here highlights the importance of understanding the genetic saturation, variation, and rate constancy spectra for the accurate calculation of divergence times by use of molecular clocks. 相似文献
4.
Circannual clocks in avian reproduction and migration 总被引:6,自引:0,他引:6
EBERHARD GWINNER 《Ibis》1996,138(1):47-63
Many behavioural and physiological functions of organisms are adjusted to the periodic changes in their environment, particularly to those related to the natural day and year. This adjustment is often achieved through the action of endogenous daily (circadian) and annual (circannual) clocks. Studies of the control of avian moult, migration and reproduction have played a major role in understanding how biological clocks function and interact with rhythms in the environment. Investigations on tropical birds such as the East African subspecies of the Stonechat ( Saxicola torquata axillaris ) and long-distance migrants like the Garden Warbler ( Sylvia boriri ) have provided the longest records of circannual rhythms, some of them running for more than 12 years, with periods ranging from about 9 to 13 months. Avian circannual rhythms are organized in a characteristic way for a particular species or population, and cross-breeding experiments have shown that some of the differences found among them are genetically determined. In African Stonechats circannual rhythms guarantee that seasonal events occur at the appropriate times of the year and in the characteristic sequence. They also control a "reproductive window" that provides the temporal framework for breeding. The width of this window is rather inflexible but the performance of a bird within this framework (e.g. whether it breeds once or twice per season) is subject to modification by environmental conditions. In migratory birds circannual programs are involved in determining the time course, distance and direction of migration. Circannual rhythms are synchronized with and modified by environmental factors in a complex way, but the endogenous mechanisms usually respond to environmental cues such that an optimal adjustment to season and latitude is guaranteed. 相似文献
5.
EBERHARD GWINNER 《Ibis》1996,138(4):47-63
Many behavioural and physiological functions of organisms are adjusted to the periodic changes in their environment, particularly to those related to the natural day and year. This adjustment is often achieved through the action of endogenous daily (circadian) and annual (circannual) clocks. Studies of the control of avian moult, migration and reproduction have played a major role in understanding how biological clocks function and interact with rhythms in the environment. Investigations on tropical birds such as the East African subspecies of the Stonechat ( Saxicola torquata axillaris ). and long-distance migrants like the Garden Warbler ( Sylvia borin ). have provided the longest records of circannual rhythms, some of them running for more than 12 years, with periods ranging from about 9 to 13 months. Avian circannual rhythms are organized in a characteristic way for a particular species or population, and cross-breeding experiments have shown that some of the differences found among them are genetically determined. In African Stonechats circannual rhythms guarantee that seasonal events occur at the appropriate times of the year and in the characteristic sequence. They also control a "reproductive window" that provides the temporal framework for breeding. The width of this window is rather inflexible but the performance of a bird within this framework (e.g. whether it breeds once or twice per season) is subject to modification by environmental conditions. In migratory birds circannual programs are involved in determining the time course, distance and direction of migration. Circannual rhythms are synchronized with and modified by environmental factors in a complex way, but the endogenous mechanisms usually respond to environmental cues such that an optimal adjustment to season and latitude is guaranteed. 相似文献
6.
Kenneth De Baets Alexandre Antonelli Philip C. J. Donoghue 《Philosophical transactions of the Royal Society of London. Series B, Biological sciences》2016,371(1699)
Evolutionary timescales have mainly used fossils for calibrating molecular clocks, though fossils only really provide minimum clade age constraints. In their place, phylogenetic trees can be calibrated by precisely dated geological events that have shaped biogeography. However, tectonic episodes are protracted, their role in vicariance is rarely justified, the biogeography of living clades and their antecedents may differ, and the impact of such events is contingent on ecology. Biogeographic calibrations are no panacea for the shortcomings of fossil calibrations, but their associated uncertainties can be accommodated. We provide examples of how biogeographic calibrations based on geological data can be established for the fragmentation of the Pangaean supercontinent: (i) for the uplift of the Isthmus of Panama, (ii) the separation of New Zealand from Gondwana, and (iii) for the opening of the Atlantic Ocean. Biogeographic and fossil calibrations are complementary, not competing, approaches to constraining molecular clock analyses, providing alternative constraints on the age of clades that are vital to avoiding circularity in investigating the role of biogeographic mechanisms in shaping modern biodiversity.This article is part of the themed issue ‘Dating species divergences using rocks and clocks’. 相似文献
7.
8.
The nature of the molecular and fossil record and their limitations must be ascertained in order to gain the most precise and accurate evolutionary timescale using genetic information. Yet the majority of such timescales are based on point estimates using fossils or the molecular clock. Here we document from the primary literature minimum and maximum fossil age estimates of the divergence of whales from artiodactyls, a commonly used anchor point for calibrating both mitogenomic and nucleogenomic placental timescales. We applied these reestimates to the most recently established placental timescale based on mitochondrial rRNA and several nuclear loci, and present an attempt to account for both genetic and fossil uncertainty. Our results indicate that disregard for fossil calibration error may inflate the power of the molecular clock when testing the time of ordinal diversification in context with the K-T boundary. However, the early history of placentals, including their superordinal diversification, remained in the Cretaceous despite a conservative approach. Our conclusions need corroboration across other frequently used fossil anchor points, but also with more genetic partitions on the linear relationship between molecular substitutions and geologic time. 相似文献
9.
Hedges SB Kumar S van Tuinen M 《BioEssays : news and reviews in molecular, cellular and developmental biology》2006,28(7):770-1; author reply 772-3
10.
Using data from primates, we show that molecular clocks in sites that have been part of a CpG dinucleotide in recent past (CpG sites) and non-CpG sites are of markedly different nature, reflecting differences in their molecular origins. Notably, single nucleotide substitutions at non-CpG sites show clear generation-time dependency, indicating that most of these substitutions occur by errors during DNA replication. On the other hand, substitutions at CpG sites occur relatively constantly over time, as expected from their primary origin due to methylation. Therefore, molecular clocks are heterogeneous even within a genome. Furthermore, we propose that varying frequencies of CpG dinucleotides in different genomic regions may have contributed significantly to conflicting earlier results on rate constancy of mammalian molecular clock. Our conclusion that different regions of genomes follow different molecular clocks should be considered when inferring divergence times using molecular data and in phylogenetic analysis. 相似文献
11.
Sumová A Bendová Z Sládek M El-Hennamy R Matejů K Polidarová L Sosniyenko S Illnerová H 《Physiological research / Academia Scientiarum Bohemoslovaca》2008,57(Z3):S139-S148
The circadian system controls the timing of behavioral and physiological functions in most organisms studied. The review addresses the question of when and how the molecular clockwork underlying circadian oscillations within the central circadian clock in the suprachiasmatic nuclei of the hypothalamus (SCN) and the peripheral circadian clocks develops during ontogenesis. The current model of the molecular clockwork is summarized. The central SCN clock is viewed as a complex structure composed of a web of mutually synchronized individual oscillators. The importance of development of both the intracellular molecular clockwork as well as intercellular coupling for development of the formal properties of the circadian SCN clock is also highlighted. Recently, data has accumulated to demonstrate that synchronized molecular oscillations in the central and peripheral clocks develop gradually during ontogenesis and development extends into postnatal period. Synchronized molecular oscillations develop earlier in the SCN than in the peripheral clocks. A hypothesis is suggested that the immature clocks might be first driven by external entraining cues, and therefore, serve as "slave" oscillators. During ontogenesis, the clocks may gradually develop a complete set of molecular interlocked oscillations, i.e., the molecular clockwork, and become self-sustained clocks. 相似文献
12.
Application of molecular clocks in ornithology revisited 总被引:1,自引:1,他引:0
A. Townsend Peterson 《Journal of avian biology》2006,37(6):541-544
Molecular clocks have seen many applications in ornithology, but many applications are uncritical. In this commentary, I point out logical inconsistencies in many uses of clocks in avian molecular systematics. I call for greater rigor in application of molecular clocks – clocks should only be used when clocklike behavior has been tested and confirmed, and when appropriate calibrations are available. Authors and reviewers should insist on such rigor to assure that systematics is indeed scientific, and not just storytelling. 相似文献
13.
We present evidence from experiments on overwintering populations of two Palearctic-Indian latitudinal migratory birds, the
black-headed bunting (Emberiza melanocephala) and the red-headed bunting (E. bruniceps), that the bird’s clock in interaction with day length regulates seasonal rhythms of migration and reproduction such that
physiological conflict between them is reduced. Initiation and termination of the body mass and testicular cycles are separately
regulated photoperiodic events. For example, under stimulatory photoperiods the response curve of body mass does not overlap
with that of the testicular growth. A response-specific photoperiodism is adaptive, since gain in body mass, critical to spring
migration, precedes gonadal recrudescence. Finally, migration as indicated by the night-time migratory restlessness under
experimental situations (e.g., intense locomotion under caged condition-called Zugunruhe) appears to be regulated by a separate circadian oscillator. 相似文献
14.
15.
Donal A. Hickey Bernhard F. Benkel Poppo H. Boer Yves Genest Sumaia Abukashawa Gerard Ben-David 《Journal of molecular evolution》1987,26(3):252-256
Summary We constructed a cDNA library for the beetle,Tribolium castaneum. This library was screened using a cloned amylase gene fromDrosophila melanogaster as a molecular probe. Beetle amylase cDNA clones were isolated from this bank, and the nucleotide sequence was obtained for a cDNA clone with a coding capacity for 228 amino acids. Both the nucleotide sequence and predicted amino acid sequence were compared to our recent results forD. melanogaster alpha-amylases, along with published sequences for other alpha-amylases. The results show that animal alpha-amylases are highly conserved over their entire length. A borader comparison, which includes plant and microbial alpha-amylase sequences, indicates that parts of the gene are conserved between prokaryotes, plants, and animals. We discuss the potential importance of this and other enzyme-coding genes for the construction of molecular phylogenies and for the study of the general question of molecular clocks in evolution. 相似文献
16.
Estimation of primate speciation dates using local molecular clocks 总被引:16,自引:0,他引:16
Protein-coding genes of the mitochondrial genomes from 31 mammalian species were analyzed to estimate the speciation dates within primates and also between rats and mice. Three calibration points were used based on paleontological data: one at 20-25 MYA for the hominoid/cercopithecoid divergence, one at 53-57 MYA for the cetacean/artiodactyl divergence, and the third at 110-130 MYA for the metatherian/eutherian divergence. Both the nucleotide and the amino acid sequences were analyzed, producing conflicting results. The global molecular clock was clearly violated for both the nucleotide and the amino acid data. Models of local clocks were implemented using maximum likelihood, allowing different evolutionary rates for some lineages while assuming rate constancy in others. Surprisingly, the highly divergent third codon positions appeared to contain phylogenetic information and produced more sensible estimates of primate divergence dates than did the amino acid sequences. Estimated dates varied considerably depending on the data type, the calibration point, and the substitution model but differed little among the four tree topologies used. We conclude that the calibration derived from the primate fossil record is too recent to be reliable; we also point out a number of problems in date estimation when the molecular clock does not hold. Despite these obstacles, we derived estimates of primate divergence dates that were well supported by the data and were generally consistent with the paleontological record. Estimation of the mouse-rat divergence date, however, was problematic. 相似文献
17.
Renner SS 《Trends in plant science》2005,10(11):550-558
Age estimation from molecular sequences has emerged as a powerful tool for inferring when a plant lineage arrived in a particular area. Knowing the tenure of lineages within a region is key to understanding the evolution of traits, the evolution of biotic interactions, and the evolution of floras. New analytical methods model change in substitution rates along individual branches of a phylogenetic tree by combining molecular data with time constraints, usually from fossils. These "relaxed clock" approaches can be applied to several gene regions that need not all have the same substitution rates, and they can also incorporate multiple simultaneous fossil calibrations. Since 1995, at least 100 plant biogeographic studies have used molecular-clock dating, and about a fifth has used relaxed clocks. Many of these report evidence of long-distance dispersal. Meta-analyses of studies from the same geographic region can identify directional biases because of prevailing wind or water currents and the relative position and size of landmasses. 相似文献
18.
Molecular clocks, molecular phylogenies and the origin of phyla 总被引:3,自引:0,他引:3
DOUGLAS H. ERWIN 《Lethaia: An International Journal of Palaeontology and Stratigraphy》1989,22(3):251-257
Erwin, Douglas H. 1989 07 15: Molecular clocks, molecular phylogenies and the origin of phyla. Lethaia , Vol. 22, pp. 251–257. Oslo. ISSN 0024–1164.
Protein, RNA and DNA sequences have been widely used to construct phylogenies and to calculate divergence times using a molecular clock. Reliance on molecular information is particularly attractive when fossil evidence is missing or equivocal, as in the Cambrian metazoan radiation. I consider the applicability of molecular clocks and phylogenetic analysis of molecular data to the origin of metazoan phyla, and conclude that molecular information is often ambiguous or misleading. Amino acid sequences are of limited use because the redundancy of the genetic code masks patterns of descent, while in a nucleotide sequence only four potential states exist at each site (the four nucleotide bases). In each case, homoplasy may often go undetected. The application of a molecular clock to resolve the timing of the metazoan radiation is unwarranted, while molecular phylogenetic reconstruction should be approached with care. A potentially more useful technique for phylogenetic reconstruction would be the use of patterns of genome structure and organization as characters. * Molecular clock, phylogenetics, metazoan radiation, origin of phyla . 相似文献
Protein, RNA and DNA sequences have been widely used to construct phylogenies and to calculate divergence times using a molecular clock. Reliance on molecular information is particularly attractive when fossil evidence is missing or equivocal, as in the Cambrian metazoan radiation. I consider the applicability of molecular clocks and phylogenetic analysis of molecular data to the origin of metazoan phyla, and conclude that molecular information is often ambiguous or misleading. Amino acid sequences are of limited use because the redundancy of the genetic code masks patterns of descent, while in a nucleotide sequence only four potential states exist at each site (the four nucleotide bases). In each case, homoplasy may often go undetected. The application of a molecular clock to resolve the timing of the metazoan radiation is unwarranted, while molecular phylogenetic reconstruction should be approached with care. A potentially more useful technique for phylogenetic reconstruction would be the use of patterns of genome structure and organization as characters. * Molecular clock, phylogenetics, metazoan radiation, origin of phyla . 相似文献
19.
Herbivores and molecular clocks as tools in plant biogeography 总被引:2,自引:0,他引:2
Olle Pellmyr James Leebens-Mack John N. Thompson 《Biological journal of the Linnean Society. Linnean Society of London》1998,63(3):367-378
Historical biogeography plays an important role in understanding evolutionary processes and the history of life, with fossil data, plate tectonics, and palaeoclimatology offering major data bases for biogeographic analyses. Here we suggest that specialized interspecific interactions, in combination with molecular data, can play an important role in such analyses. We use the interaction between Bowlesia incana (Apiaceae) and the host-specific herbivore Greya powelli (Lepidoptera: Prodoxidae) in California to demonstrate the utility. Distributed in disjunct temperate parts of North and South America, B. incana has been proposed to have been introduced in historical time (<250 yrs BP) into North America. Three lines of evidence together suggest that the plant is of a far older age in North America. First, G. powelli is not known from the South American range and the genus is very unlikely to exist there, making introduction with the plant in North America unlikely. Second, divergence of mtDNA among members of the genus Greya suggests that the lineage leading to G. powelli originated 2.3-3.8 Mya, thus predating a proposed introduction by several orders of magnitude. Third, host shifts are consistently linked with species divergence within the genus Greya, suggesting that the G. powelli lineage has utilized Bowlesia since a time near its origin. We conclude that B. incana has been present in western North America for a long period of time, and that it did not arrive by human transport. The use of specialized herbivores and molecular data adds a powerful tool to historical plant biogeography. 相似文献
20.
David S. Hibbett 《Journal of Biogeography》2001,28(2):231-241