scholarly journals Rewinding the molecular clock in the genus Carabus (Coleoptera: Carabidae) in light of fossil evidence and the Gondwana split: A reanalysis

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0256679
Author(s):  
Lars Opgenoorth ◽  
Sylvia Hofmann ◽  
Joachim Schmidt
Keyword(s):  
Molecular Clock ◽  
Nuclear Dna ◽  
Molecular Clocks ◽  
Nuclear Markers ◽  
New Approach ◽  
Root Age ◽  
Fossil Evidence ◽  
Outgroup Taxon ◽  
Nd5 Gene ◽  
Sufficient Set

Molecular clocks have become powerful tools given increasing sequencing and fossil resources. However, calibration analyses outcomes depend on the choice of priors. Here, we revisited the seminal dating study published by Andújar and coworkers of the genus Carabus proposing that prior choices need re-evaluation. We hypothesized that reflecting fossil evidence and the Gondwanan split properly significantly rewinds the molecular clock. We re-used the dataset including five mitochondrial and four nuclear DNA fragments with a total length of 7888 nt. Fossil evidence for Oligocene occurrence of Calosoma was considered. Root age was set based on the fossil evidence of Harpalinae ground beetles in the Upper Cretaceous. Paleogene divergence of the outgroup taxa Ceroglossini and Pamborini is introduced as a new prior based on current paleontological and geological literature. The ultrametric time-calibrated tree of the extended nd5 dataset resulted in a median TMRCA Carabus of 53.92 Ma (HPD 95% 45.01–63.18 Ma), roughly 30 Ma older than in the Andújar study. The splits among C. rugosus and C. morbillosus (A), C. riffensis from the European Mesocarabus (B), and Eurycarabus and Nesaeocarabus (C) were dated to 17.58 (12.87–22.85), 24.14 (18.02–30.58), and 21.6 (16.44–27.43) Ma. They were decidedly older than those previously reported (7.48, 10.93, and 9.51 Ma). These changes were driven almost entirely by constraining the Carabidae time-tree root with a Harpalinae amber fossil at ~99 Ma. Utilizing the nd5 dating results of three well-supported Carabus clades as secondary calibration points for the complete MIT-NUC dataset led to a TMRCA of Carabus of 44.72 (37.54–52.22) Ma, compared with 25.16 Ma (18.41–33.04 Ma) in the previous study. Considering fossil evidence for Oligocene Calosoma and Late Cretaceous Harpalini together with the Gondwanan split as a new prior, our new approach supports the origin of genus Carabus in the Eocene. Our results are preliminary because of the heavy reliance on the nd5 gene, and thus will have to be tested with a sufficient set of nuclear markers. Additionally, uncertainties due to dating root age of the tree based on a single fossil and outgroup taxon affect the results. Improvement of the fossil database, particularly in the supertribe Carabitae, is needed to reduce these uncertainties in dating Carabus phylogeny.

scholarly journals Rewinding the molecular clock in the genus Carabus (Coleoptera: Carabidae) in light of fossil evidence and the Gondwana split: a re-analyses

2020 ◽  
Author(s):  
Lars Opgenoorth ◽  
Sylvia Hofmann ◽  
Joachim Schmidt
Keyword(s):  
Molecular Clock ◽  
Nuclear Dna ◽  
Major Effect ◽  
Molecular Clocks ◽  
Data Set ◽  
Root Age ◽  
Fossil Evidence ◽  
Outgroup Taxon ◽  
Nd5 Gene ◽  
Fossil Data

1AbstractBackgroundMolecular clocks have become powerful tools given increasing sequencing and fossil resources. However, outcome of calibration analyses depend on choosing priors. Here we revisit a seminal dating study of the genus Carabus by Andujar et al. proposing that their prior choices need re-evaluation with the hypothesis that reflecting fossil evidence and the Gondwanan split properly rewinds the molecular clock significantly. We used the same dataset including five mitochondrial and four nuclear DNA fragments with 7888 nt total length. We set the root age based on the fossil evidence of Harpalinae ground beetles in the Upper Cretaceous and introduce the Paleogene divergence of the outgroup taxa Ceroglossus (endemic to South-America) and Pamborus + Maoripamborus (Australia, New Zealand) as a new prior based on current paleontological and geological literature.ResultsThe ultrametric time-calibrated tree of the extended nd5 dataset resulted in a median TMRCA Carabus age of 58.48 Ma (HPD95% 46.61-72.04), roughly 35 Ma older than in the Andujar study. The splits between C. rugosus and C. morbillosus (A), between C. riffensis from the European Mesocarabus (B), and between Eurycarabus and Nesaeocarabus (C) were dated to 19.19 (13.54-25.87), 25.95 (18.8-34.62), and 23.98 (17.28-31.47) Ma and were thus decidedly older than previously reported (7.48, 10.93, and 9.51 Ma). These changes were driven solely by constraining the Carabidae time tree root with Harpalinae amber fossils at ∼99 Ma. Utilizing the nd5 dating results of three well supported Carabus clades as secondary calibration points for the complete MIT-NUC data set lead to a TMRCA of Carabus of 53.56 (41.25-67.05) Ma compared to 25.16 (18.41-33.04) in Andujar’s study.ConclusionTaking into account the Gondwanan split as a new prior, together with the fossil evidence of the outgroup taxon Harpalini in the Late Cretaceous, our new approach supports an origin of the genus Carabus in the Paleocene-Early Eocene. Our results are preliminary due to the heavy reliance on the nd5 gene and thus will have to be tested with sufficient set of nuclear markers. In addition, uncertainties arise from dating the root age of the tree based on a single fossil and outgroup taxon which has a major effect on the results. Improvement of the fossil data base particularly in the supertribe Carabitae is thus strongly needed to reduce the currently large uncertainties in dating Carabus phylogeny.

scholarly journals Tips and nodes are complementary not competing approaches to the calibration of molecular clocks

2016 ◽  
Vol 12 (4) ◽  
pp. 20150975 ◽  
Author(s):  
Joseph E. O'Reilly ◽  
Philip C. J. Donoghue
Keyword(s):  
Molecular Clock ◽  
Divergence Time ◽  
Molecular Clocks ◽  
Fossil Species ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Fossil Evidence ◽  
Accuracy And Precision ◽  
Age Constraints ◽  
Age Estimates

Molecular clock methodology provides the best means of establishing evolutionary timescales, the accuracy and precision of which remain reliant on calibration, traditionally based on fossil constraints on clade (node) ages. Tip calibration has been developed to obviate undesirable aspects of node calibration, including the need for maximum age constraints that are invariably very difficult to justify. Instead, tip calibration incorporates fossil species as dated tips alongside living relatives, potentially improving the accuracy and precision of divergence time estimates. We demonstrate that tip calibration yields node calibrations that violate fossil evidence, contributing to unjustifiably young and ancient age estimates, less precise and (presumably) accurate than conventional node calibration. However, we go on to show that node and tip calibrations are complementary, producing meaningful age estimates, with node minima enforcing realistic ages and fossil tips interacting with node calibrations to objectively define maximum age constraints on clade ages. Together, tip and node calibrations may yield evolutionary timescales that are better justified, more precise and accurate than either calibration strategy can achieve alone.

Central and Peripheral Clock Control of Circadian Feeding Rhythms

2021 ◽  
pp. 074873042110458
Author(s):  
Carson V. Fulgham ◽  
Austin P. Dreyer ◽  
Anita Nasseri ◽  
Asia N. Miller ◽  
Jacob Love ◽  
...  
Keyword(s):  
Locomotor Activity ◽  
Circadian Clock ◽  
Feeding Behavior ◽  
Molecular Clock ◽  
Fat Body ◽  
Molecular Clocks ◽  
Central Brain ◽  
Feeding Rhythms ◽  
Free Running ◽  
The Brain

Many behaviors exhibit ~24-h oscillations under control of an endogenous circadian timing system that tracks time of day via a molecular circadian clock. In the fruit fly, Drosophila melanogaster, most circadian research has focused on the generation of locomotor activity rhythms, but a fundamental question is how the circadian clock orchestrates multiple distinct behavioral outputs. Here, we have investigated the cells and circuits mediating circadian control of feeding behavior. Using an array of genetic tools, we show that, as is the case for locomotor activity rhythms, the presence of feeding rhythms requires molecular clock function in the ventrolateral clock neurons of the central brain. We further demonstrate that the speed of molecular clock oscillations in these neurons dictates the free-running period length of feeding rhythms. In contrast to the effects observed with central clock cell manipulations, we show that genetic abrogation of the molecular clock in the fat body, a peripheral metabolic tissue, is without effect on feeding behavior. Interestingly, we find that molecular clocks in the brain and fat body of control flies gradually grow out of phase with one another under free-running conditions, likely due to a long endogenous period of the fat body clock. Under these conditions, the period of feeding rhythms tracks with molecular oscillations in central brain clock cells, consistent with a primary role of the brain clock in dictating the timing of feeding behavior. Finally, despite a lack of effect of fat body selective manipulations, we find that flies with simultaneous disruption of molecular clocks in multiple peripheral tissues (but with intact central clocks) exhibit decreased feeding rhythm strength and reduced overall food intake. We conclude that both central and peripheral clocks contribute to the regulation of feeding rhythms, with a particularly dominant, pacemaker role for specific populations of central brain clock cells.

Understanding Molecular Clocks and Time Trees

2021 ◽  
pp. 326-337
Author(s):  
Andrew V. Z. Brower ◽  
Randall T. Schuh
Keyword(s):  
Amino Acid ◽  
Molecular Clock ◽  
Significant Error ◽  
Evolutionary Tree ◽  
Molecular Clocks ◽  
Amino Acid Substitutions ◽  
Absolute Minimum ◽  
Short Time ◽  
Over Time ◽  
Age Estimates

This chapter examines molecular clocks and time trees. Although laden with numerous process assumptions that may or may not be true (or knowable), the idea is appealingly straightforward: if amino acid substitutions in proteins occurred at a relatively steady pace that were more or less constant both over time and along each of the branches of a diverging evolutionary tree, then the number of substitutions would be directly related to the time since the taxa in question diverged from one another. However, evidence does not support a universal molecular clock. Evidence might or might not support “local” clocklike evolution among closely related taxa over relatively short time spans. Although absolute minimum ages for clades may be inferred from fossils, from biogeographical patterns, or extrapolated from secondary calibrations, such age estimates are subject to potentially significant error due to vagaries of geological dating as well as ambiguities of fossil identity. The test of a time tree hypothesis is to discover new fossil evidence that corroborates or falsifies it.

Mitochondrial lineages or discrete species? Assessing diversity within Timon tangitanus (Lacertidae) using mitochondrial and nuclear DNA sequences

2020 ◽  
Vol 41 (1) ◽  
pp. 123-132
Author(s):  
João M. Abreu ◽  
Daniele Salvi ◽  
Ana Perera ◽  
D. James Harris
Keyword(s):  
North Africa ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Sequence Divergence ◽  
Lineage Sorting ◽  
Lizard Species ◽  
Nuclear Markers ◽  
Species Complexes ◽  
Mtdna Sequence ◽  
Mtdna Lineages

Abstract Identification of extremely high levels of mitochondrial DNA (mtDNA) sequence divergence within reptiles from North Africa is commonplace. This high divergence often compares with interspecific levels among widely accepted species, leading to the hypothesis of the occurrence of species complexes. Indeed, in many examples, data from nuclear markers support such taxonomic recognition. Such is the case of two recently recognized ocellated lizard species of the genus Timon, T. nevadensis, from Spain, and T. kurdistanicus, from the Middle East, which both showed notable genetic differentiation from their sister taxa. In North Africa, highly divergent mtDNA lineages of Timon tangitanus were previously identified but not corroborated with nuclear markers. Here we expand geographic sampling across the range of Timon tangitanus and complement mtDNA sequences with data from nuclear markers (MC1R and ACM4). We identify four divergent mtDNA lineages, at a level similar to some reptile species. However, the nuclear markers show limited differentiation and lack of lineage sorting. This and some other recent assessments within reptiles discourage the use of mtDNA data alone as a proxy for taxonomic units, demonstrating once more the need for integrative taxonomic approaches.

scholarly journals A fresh look at the fossil evidence for early Archaean cellular life

2006 ◽  
Vol 361 (1470) ◽  
pp. 887-902 ◽  
Author(s):  
Martin Brasier ◽  
Nicola McLoughlin ◽  
Owen Green ◽  
David Wacey
Keyword(s):  
Critical Analysis ◽  
Fossil Record ◽  
Volcanic Glass ◽  
New Approach ◽  
Microbial Origin ◽  
Cellular Life ◽  
Fossil Evidence ◽  
Rock Record ◽  
Inclusion Trails ◽  
Self Organizing

The rock record provides us with unique evidence for testing models as to when and where cellular life first appeared on Earth. Its study, however, requires caution. The biogenicity of stromatolites and ‘microfossils’ older than 3.0 Gyr should not be accepted without critical analysis of morphospace and context, using multiple modern techniques, plus rejection of alternative non-biological (null) hypotheses. The previous view that the co-occurrence of biology-like morphology and carbonaceous chemistry in ancient, microfossil-like objects is a presumptive indicator of biogenicity is not enough. As with the famous Martian microfossils, we need to ask not ‘what do these structures remind us of?’, but ‘what are these structures?’ Earth's oldest putative ‘microfossil’ assemblages within 3.4–3.5 Gyr carbonaceous cherts, such as the Apex Chert, are likewise self-organizing structures that do not pass tests for biogenicity. There is a preservational paradox in the fossil record prior to ca 2.7 Gyr: suitable rocks (e.g. isotopically light carbonaceous cherts) are widely present, but signals of life are enigmatic and hard to decipher. One new approach includes detailed mapping of well-preserved sandstone grains in the ca 3.4 Gyr Strelley Pool Chert. These can contain endolithic microtubes showing syngenicity, grain selectivity and several levels of geochemical processing. Preliminary studies invite comparison with a class of ambient inclusion trails of putative microbial origin and with the activities of modern anaerobic proteobacteria and volcanic glass euendoliths.

scholarly journals Diversification dynamics of total-, stem-, and crown-groups are compatible with molecular clock estimates of divergence times

2021 ◽  
Vol 7 (24) ◽  
pp. eabf2257
Author(s):  
Alan J. S. Beavan ◽  
Davide Pisani ◽  
Philip C. J. Donoghue
Keyword(s):  
Time Scales ◽  
Molecular Clock ◽  
Fossil Record ◽  
Divergence Times ◽  
Evolutionary Time ◽  
Crown Group ◽  
Total Group ◽  
Fossil Evidence ◽  
Evolutionary Radiations ◽  
Birth Death

Molecular evolutionary time scales are expected to predate the fossil evidence, but, particularly for major evolutionary radiations, they can imply extremely protracted stem lineages predating the origin of living clades, leading to claims of systematic overestimation of divergence times. We use macroevolutionary birth-death models to describe the range of total-group and crown-group ages expected under constant rates of speciation and extinction. We extend current predictions on origination times for crown- and total-groups, and extinction of stem-groups, demonstrating that there is broad variance in these predictions. Under constant rates of speciation and extinction, we show that the distribution of expected arthropod total-group ages is consistent with molecular clock estimates. The fossil record cannot be read literally, and our results preclude attempts to interpret the antiquity of clades based on the co-occurrence of stem- and crown-representatives.

scholarly journals Cas9/gRNA-mediated genome editing of yeast mitochondria and Chlamydomonas chloroplasts

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8362 ◽  
Author(s):  
Byung-Chun Yoo ◽  
Narendra S. Yadav ◽  
Emil M. Orozco ◽  
Hajime Sakai
Keyword(s):  
Genome Editing ◽  
Nuclear Dna ◽  
Integration Site ◽  
Repair System ◽  
Yeast Mitochondria ◽  
New Approach ◽  
Chloroplast Genomes ◽  
Wide Range ◽  
Nhej Repair ◽  
Target Sites

We present a new approach to edit both mitochondrial and chloroplast genomes. Organelles have been considered off-limits to CRISPR due to their impermeability to most RNA and DNA. This has prevented applications of Cas9/gRNA-mediated genome editing in organelles while the tool has been widely used for engineering of nuclear DNA in a number of organisms in the last several years. To overcome the hurdle, we designed a new approach to enable organelle genome editing. The plasmids, designated “Edit Plasmids,” were constructed with two expression cassettes, one for the expression of Cas9, codon-optimized for each organelle, under promoters specific to each organelle, and the other cassette for the expression of guide RNAs under another set of promoters specific to each organelle. In addition, Edit Plasmids were designed to carry the donor DNA for integration between two double-strand break sites induced by Cas9/gRNAs. Each donor DNA was flanked by the regions homologous to both ends of the integration site that were short enough to minimize spontaneous recombination events. Furthermore, the donor DNA was so modified that it did not carry functional gRNA target sites, allowing the stability of the integrated DNA without being excised by further Cas9/gRNAs activity. Edit Plasmids were introduced into organelles through microprojectile transformation. We confirmed donor DNA insertion at the target sites facilitated by homologous recombination only in the presence of Cas9/gRNA activity in yeast mitochondria and Chlamydomonas chloroplasts. We also showed that Edit Plasmids persist and replicate in mitochondria autonomously for several dozens of generations in the presence of the wild-type genomes. Finally, we did not find insertions and/or deletions at one of the Cas9 cleavage sites in Chloroplasts, which are otherwise hallmarks of Cas9/gRNA-mediated non-homologous end joining (NHEJ) repair events in nuclear DNA. This is consistent with previous reports of the lack of NHEJ repair system in most bacteria, which are believed to be ancestors of organelles. This is the first demonstration of CRISPR-mediated genome editing in both mitochondria and chloroplasts in two distantly related organisms. The Edit Plasmid approach is expected to open the door to engineer organelle genomes of a wide range of organisms in a precise fashion.

scholarly journals The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates

2018 ◽  
Author(s):  
Brice A. J. Sarver ◽  
Matthew W. Pennell ◽  
Joseph W. Brown ◽  
Sara Keeble ◽  
Kayla M. Hardwick ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Substitution Rate ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Parameter Estimates ◽  
Molecular Clocks ◽  
Estimation Of Parameters ◽  
Rate Heterogeneity ◽  
Diversification Rates ◽  
The Impact

AbstractComparative methods allow researchers to make inferences about evolutionary processes and patterns from phylogenetic trees. In Bayesian phylogenetics, estimating a phylogeny requires specifying priors on parameters characterizing the branching process and rates of substitution among lineages, in addition to others. However, the effect that the selection of these priors has on the inference of comparative parameters has not been thoroughly investigated. Such uncertainty may systematically bias phylogenetic reconstruction and, subsequently, parameter estimation. Here, we focus on the impact of priors in Bayesian phylogenetic inference and evaluate how they affect the estimation of parameters in macroevolutionary models of lineage diversification. Specifically, we use BEAST to simulate trees under combinations of tree priors and molecular clocks, simulate sequence data, estimate trees, and estimate diversification parameters (e.g., speciation rates and extinction rates) from these trees. When substitution rate heterogeneity is large, parameter estimates deviate substantially from those estimated under the simulation conditions when not captured by an appropriate choice of relaxed molecular clock. However, in general, we find that the choice of tree prior and molecular clock has relatively little impact on the estimation of diversification rates insofar as the sequence data are sufficiently informative and substitution rate heterogeneity among lineages is low-to-moderate.

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