Teasing Apart Molecular- Versus Fossil-based Error Estimates when Dating Phylogenetic Trees: A Case Study in the Birch Family (Betulaceae)

  title={Teasing Apart Molecular- Versus Fossil-based Error Estimates when Dating Phylogenetic Trees: A Case Study in the Birch Family (Betulaceae)},
  author={F{\'e}lix Forest and Vincent Savolainen and Mark W. Chase and Richard Lupia and Anne Bruneau and Peter R. Crane},
Abstract Fossils are widely used as calibration points in molecular-based dating studies, but their placement on a phylogenetic tree of extant species is always highly problematic. We explore some of the problems linked to calibration with fossils, in particular their position on the tree, and emphasize the use of multiple calibration points to obtain better estimates. We use a phylogenetic analysis of Betulaceae based on nuclear ribosomal DNA sequences (5S spacer and ITS) as a case study and… 

Integrating fossils in a molecular‐based phylogeny and testing them as calibration points for divergence time estimates in Menispermaceae

The use of Prototinomiscium as a dating constraint for Menispermaceae appears to be a conservative approach and can also account for rate heterogeneity among lineages.

Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales).

It is suggested that increased background research should be made at all stages of the calibration process to reduce errors wherever possible, from verifying the geochronological data on the fossils to critical reassessment of their phylogenetic position.

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  • F. Forest
  • Environmental Science, Geography
    Annals of botany
  • 2009
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Phylogeny of extant and fossil Juglandaceae inferred from the integration of molecular and morphological data sets.

The results clearly show that the amount of missing data in any given taxon is not by itself an operational guideline for excluding fossils from analysis, and each of the methods provided reasonable placement of both fossils and simulated "artificial fossils" in the phylogeny previously inferred only from extant taxa.

A comparative study in ancestral range reconstruction methods: retracing the uncertain histories of insular lineages.

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Harvesting Betulaceae sequences from GenBank to generate a new chronogram for the family

The fossil record and molecular clocks calibrated with alternating fossils indicate that the stem lineage of Betulaceae dates back to the Upper Cretaceous, the two subfamilies to the Palaeocene and the most recent common ancestors of each of the living genera to the mid- to late Miocene.

The complete chloroplast genomes of three Betulaceae species: implications for molecular phylogeny and historical biogeography

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Phylotranscriptomic analyses in plants using Betulaceae as an example

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Plastomes of Betulaceae and phylogenetic implications

The dating analysis, based on four fossils, suggests that the most recent common ancestors of the extant genera date back to the mid‐ to late Miocene, and confirms that Betulaceae started to diversify in the upper Cretaceous/early Paleocene.


  • M. RybergP. B. Matheny
  • Biology, Environmental Science
    Evolution; international journal of organic evolution
  • 2011
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Sources of error and confidence intervals in estimating the age of angiosperms from rbcL and 18S rDNA data.

Approximate 95% confidence intervals on ages are wider for rbcL than 18S, ranging up to 160 my for phylogenetic uncertainty, 90 my for substitutional noise, and 70 my for lineage effects, as well as some estimates from previous molecular studies.

Molecular clocks and the incompleteness of the fossil record

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Assessing the Reliability of 5S rRNA Sequence Data for Phylogenetic Analysis in Green Plants

The results demonstrate that phylogenetic estimates based only on analyses of 5S rRNA sequences must be viewed with considerable caution, and that bootstrapping provides little statistical support for most of these groupings.

Evolution of the angiosperms: calibrating the family tree

Angiosperm divergence times are estimated using non–parametric rate smoothing and a three–gene dataset covering ca.


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  • Economics
    Evolution; international journal of organic evolution
  • 1985
The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.

A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy

A new method for estimating divergence times when evolutionary rates are variable across lineages is proposed. The method, called nonparametric rate smoothing (NPRS), relies on minimization of

Phylogenies and angiosperm diversification

Cladistic evidence that Pentoxylon, Bennettitales, and Gnetales are the sister group of angiosperms implies that the angiosperm line (angiophytes) existed by the Late Triassic, and "Tree-thinking" clarifies discussions of the age of groups, by distinguishing between splitting of the stem-lineage from its sister group and splits of the crown-group into extant clades.

Complete congruence between morphological and rbcL-based molecular phylogenies in birches and related species (Betulaceae).

The topologies obtained by the different methods were completely congruent, and bootstrapping strongly supported the division of the family Betulaceae into two major clades, Betuleae (Alnus and Betula) and Coryleae (other members).

Phylogeny of the eudicots : a nearly complete familial analysis based on rbcL gene sequences

A phylogenetic analysis of 589 plastid rbcL gene sequences representing nearly all eudicot families was performed, and bootstrap re-sampling was used to assess support for clades.