Molecular Phylogeny

Molecular phylogeny rocks.

Basically, you look at corresponding DNA segments in different kinds of animals, and based on the similarities and subtle variations between them, you can infer their commonality of ancestry. Since this is based directly on the DNA, it's more definitive than the old way, which is based on careful comparisons of bones, teeth and anatomy -- which is usually accurate, but can be fooled by, for instance, convergent evolution.

There were two broad investigations reported recently in Nature that led to a better understanding of the family tree of placental mammals. In some cases, groups were shifted around -- for instance, carnivores are grouped with dolphins and whales, while primates are now placed closer to rodents.

The timing of the divergences within groups also appears to be linked with continental shifts -- so we can see the continents breaking up and giving rise to various large groupings of animals.

Here is more reading:

Springer, M.S et al. Parallel adaptive radiations in two major clades of placental mammals. Nature 409, 610-614 (2001). Abstract:


 * Higher level relationships among placental mammals, as well as the historical biogeography and morphological diversification of this group, remain unclear. Here we analyse independent molecular data sets, having aligned lengths of DNA of 5,708 and 2,947 base pairs, respectively, for all orders of placental mammals. Phylogenetic analyses resolve placental orders into four groups: Xenarthra, Afrotheria, Laurasiatheria, and Euarchonta plus Glires. The first three groups are consistently monophyletic with different methods of analysis. Euarchonta plus Glires is monophyletic or paraphyletic depending on the phylogenetic method. A unique nine-base-pair deletion in exon 11 of the BRCA1 gene provides additional support for the monophyly of Afrotheria, which includes proboscideans, sirenians, hyracoids, tubulidentates, macroscelideans, chrysochlorids and tenrecids. Laurasiatheria contains cetartiodactyls, perissodactyls, carnivores, pangolins, bats and eulipotyphlan insectivores. Parallel adaptive radiations have occurred within Laurasiatheria and Afrotheria. In each group, there are aquatic, ungulate and insectivore-like forms.

O'Brien, S.J. et al. Molecular phylogenetics and the origins of placental mammals. Nature 409, 614-618 (2001). Abstract:


 * The precise hierarchy of ancient divergence events that led to the present assemblage of modern placental mammals has been an area of controversy among morphologists, palaeontologists and molecular evolutionists. Here we address the potential weaknesses of limited character and taxon sampling in a comprehensive molecular phylogenetic analysis of 64 species sampled across all extant orders of placental mammals. We examined sequence variation in 18 homologous gene segments (including nearly 10,000 base pairs) that were selected for maximal phylogenetic informativeness in resolving the hierarchy of early mammalian divergence. Phylogenetic analyses identify four primary superordinal clades: (I) Afrotheria (elephants, manatees, hyraxes, tenrecs, aardvark and elephant shrews); (II) Xenarthra (sloths, anteaters and armadillos); (III) Glires (rodents and lagomorphs), as a sister taxon to primates, flying lemurs and tree shrews; and (IV) the remaining orders of placental mammals (cetaceans, artiodactyls, perissodactyls, carnivores, pangolins, bats and core insectivores). Our results provide new insight into the pattern of the early placental mammal radiation.

An overview of the two reports and what they mean, from Nature: http://www.nature.com/nsu/010201/010201-11.html

A news article about one of the reports: http://www.save-the-elephants.org/2001%20web%20stories/Geog%20more%20than%20Bio.htm

Cladograms based on the two reports: http://www.fmnh.helsinki.fi/users/haaramo/Metazoa/Deuterostoma/Chordata/Synapsida/Eutheria/Eutheria_3.htm, http://www.fmnh.helsinki.fi/users/haaramo/Metazoa/Deuterostoma/Chordata/Synapsida/Eutheria/Eutheria_4.htm

Parsimony and molecular phylogeny -- how do you reconstruct a rational hierarchy of changes when all you have are the tips of the tree branches? http://helix.biology.mcmaster.ca/721/outline2/node50.html

And for the advanced reader:

A searchable database of accumulated DNA segments from many sources, so you can create your own parsimonious trees: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Popset

...using something like this tool: http://www.multimedialibrary.com/Phylogenator.html