Relaxed phylogenetics and dating with confidence plos biology

Unfortunately, this approach underestimates the amount of evolutionary change because it does not account for the fact that each site may change more than once during evolutionary history.

Statistical tools, called nucleotide or amino acid substitution models, are therefore used to estimate genetic distances between sequences.

speed dating 40 ans plus - Relaxed phylogenetics and dating with confidence plos biology

There is a bewildering hierarchy of substitution models available, each making a different and specific set of assumptions about the evolutionary process of sequence change [ 2].

The simplest models assume that all types of mutation are equivalent and that all sites in a sequence change at the same rate.

The degree to which a model fits the data at hand (accuracy) is always improved by adding more parameters (complexity), but since the amount of data remains constant the statistical uncertainty about each parameter increases.

In addition, the biological meaning of each parameter becomes harder to decipher so the explanatory power of the model decreases ( ).

The ubiquitous and highly diverse element Australian Acacia makes an ideal candidate for investigating a range of questions about the evolution of the flora of continental Australia.

In the past, such efforts have been hampered by a lack of well-supported phylogenies and by the relatively poor macrofossil record, which probably reflects the depositional environment in which Acacia species are predominantly found.

The lengths of the branches in the phylogeny thus represent estimated numbers of sequence changes ( However, genetic distances are rather crude indicators of evolutionary history.

A small genetic distance between two sequences may suggest a recent common ancestor, but is also consistent with a slower rate of sequence change and a more ancient common ancestor (i.e., genetic distance = evolutionary rate × time).

By using multiple reliable fossil constraints, we applied a combination of primary calibration points to produce a comprehensive study of divergence dates in Acacia s.s. Previous dating studies included very limited samples of the diversity of Australian Acacia and experienced difficulties in identifying appropriate age calibrations for the lineage, leading to considerable variation in their results.

We used novel calibration schemes and multiple nuclear and chloroplast DNA sequence markers to produce the first estimates of divergence dates for major lineages within the Australian Acacia s.s.

Whatever the source of the independent information, it is usual to calibrate a phylogeny by assuming that all its branches evolve at the same rate—i.e., there is a constant but stochastic “molecular clock” of sequence change.

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