Phylogenetics and dating with definition of dating exclusively
Our algorithms exploit the tree (recursive) structure of the problem at hand, and the close relationships between least-squares and linear algebra.
We distinguish between an unconstrained setting and the case where the temporal precedence constraint (i.e., an ancestral node must be older that its daughter nodes) is accounted for.
Phylogenies provide a useful way to understand the evolutionary history of genetic samples, and data sets with more than a thousand taxa are becoming increasingly common, notably with viruses (e.g., human immunodeficiency virus (HIV)).
Dating ancestral events is one of the first, essential goals with such data.
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Proceedings of the National Academy of Sciences 1842-18847. Philosophical Transactions of the Royal Society of London B 377-1483. Ariati SR, Murphy DJ, Udovicic F, Ladiges PY (2006) Molecular phylogeny of three groups of acacias (Acacia subgenus Phyllodineae) in arid Australia based on the internal and external transcribed spacer regions of nr DNA. | Cross Ref | Acacia subgenus Phyllodineae) in arid Australia based on the internal and external transcribed spacer regions of nr DNA.&title=Systematics and Biodiversity&date=2006&volume=4&spage=417&epage=426&sid=csiro&aulast=Ariati&aufirst=SR" target="_blank" Bouchenak-Khelladi Y, Maurin O, Hurter J, van der Bank M (2010) The evolutionary history and biogeography of Mimosoideae (Leguminosae): An emphasis on African acacias. Australian Systematic Botany 16, 27–33.| CAS | Acacia subgenera Acacia and Aculeiferum (Fabaceae: Mimosoideae), based on the chloroplast mat K coding sequence and flanking trn K intron spacer regions.&title=Australian Systematic Botany&date=2003&volume=16&spage=27&epage=33&sid=csiro&aulast=Miller&aufirst=JT" target="_blank" Miller JT, Burd M (2013) Australia’s Acacia: unrecognized convergent evolution.Molecular Phylogenetics and Evolution 57, 495–508.| Brown GK, Ariati SR, Murphy DJ, Miller JTH, Ladiges PY (2006) Bipinnate acacias (Acacia subg. Botrycephalae) of eastern Australia are polyphyletic based on DNA sequence data. (CSIRO Publishing: Melbourne) Miller JT, Bayer RJ (2000) Molecular phylogenetics of Acacia (Fabaceae: Mimosoideae) based on chloroplast Trn K/Mat K and nuclear histone H3-D sequences. In ‘Invasion biology and ecosystem theory; insights from a continent in transformation’. (Cambridge University Press: Cambridge) Miller JT, Andrew R, Bayer RJ (2003a) Molecular phylogenetics of the Australian acacias of subg.However, the broader subfamily Mimosoideae offers several reliably age-constrained fossils that can be used as calibrations in divergence-dating analyses of DNA sequence data.In addition, the microfossil pollen record of Acacia is relatively rich and provides a good age constraint for the entire Acacia clade.
Even with more sophisticated relaxed-clock analyses, nodes that are distant from fossil calibrations will have a very high uncertainty in dating.