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.

Calibrating the Tree of Life: fossils, molecules and evolutionary timescales.

  • F. Forest
  • Environmental Science, Geography
    Annals of botany
  • 2009
The fossil record remains the most reliable source of information for the calibration of phylogenetic trees, although associated assumptions and potential bias must be taken into account.

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.

Likelihood-based estimates of ancestral ranges for Cyrtandra suggest a major dispersal route into the Pacific through the islands of Fiji and Samoa, motivating future biogeographic investigation of this poorly known region.

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

This research elucidates the potential of chloroplast genome sequences in the application of developing molecular markers, studying evolutionary relationships and historical dynamic of Betulaceae, and reveals the advantages of using chlorop last genome data to illuminate those phylogenies that have not been well solved yet by traditional approaches in other plants.

Phylotranscriptomic analyses in plants using Betulaceae as an example

Phylogenetic relationships within the Betulaceae family, largely consistent with those previously based on chloroplast DNA and nuclear internal transcribed spacer sequence variations, received high support for all clades and subclades, but it was found that support values for the sister relationship between two polyploid genera were lower than those between diploid groups if only a few orthologs were sampled.

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
It is suggested that continuous diversification in the Hebelomateae has been facilitated by climatic and vegetation changes throughout the Cenozoic, and is cautioned against modeling multiple genes as a single partition when performing phylogenetic dating analyses.



Rate heterogeneity among lineages of tracheophytes: Integration of molecular and fossil data and evidence for molecular living fossils

This study minimize the potential error caused by inaccurate topology and uncertain calibration times by using a well-supported tree, multiple genes, and multiple well-substantiated dates to explore the correspondence between the fossil record and molecular-based age estimates for major clades of tracheophytes.

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

This analysis brings relative- and absolute-rate tests into accord and test the null hypothesis that seemingly disparate rates of molecular evolution are in fact equal under the simplifying assumption that fossils are randomly and independently distributed over their temporal ranges and that fossils can be accurately placed in a phylogenetic context.

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.


  • J. Felsenstein
  • 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).