What is evolution? (part 2)

When an organism's genome has changed, in comparison with those of its parent(s), and when that change propagates within a population, evolution may be said to be occurring in the population. Are long term fixations of traits in populations the quanta of evolution? Some changes have no observable effect on the life of the organism, some have visible effects, and some change the organism's reproductive system or behaviour. Groups of organisms evolve which mate very slightly differently from the rest of the population, or are reproductively or ecologically isolated. Over the generations this leads groups which mate more often with each other to resemble each other more than the rest of the population, and to gradually drift, genetically, further from the main population to the point where their DNA no longer recombines with that of the rest of the population at all (or at least very very infrequently). We then might say that there are two species, and a reproductively isolated group of individuals is one of the ways that people have approached the definition of what a species is. The species model maybe the subject of a future blog.

Looking back from the current organisms that are alive, and trying to decipher when the branches occurred - the 'speciation events' that separated ancestral populations into reproductively isolated clades - is the subject of much research and scientific interest. In the plant world, the recent work by Moore et al., 2007 (no relation) develops modern phylogenetic analyses of chloroplast genomic data from angiosperms (flowering plants broadly), in an effort to clarify the basal branching order. They concluded that a rapid basal expansion occurred between 143.8+-4.8 and 140.3+-4.8 Mya, and found support through multiple maximum likelihood analyses for a number of hypotheses of branching order. This time coincides with the Early Cretaceous Berriasian epoch. This epoch was characterised by continued cooling including glaciation at high altitudes, and increased tropical humidity, during the break up of Gondwana, and is overlapped by estimates of the timing of the 1R plant genome duplication, identified in Arabidopsis (DeBodt et al., 2005).

In the animal clade, I read some really interesting work by McPeek and Brown (2007) recently. They integrated molecular and fossil phylogenetic data sets to address the question of whether species richness in a clade is best accounted for by clade age or clade diversification rate. They found that, in animals, clade age is the dominant signal in clade species richness. It will be interesting to see whether the same holds true for plants. I really felt for the researcher who measured all the pictures of trees with calipers. Hopefully, the very recently published work of Laubach and von Haeseler (2007) will make a useful contribution to future studies of this type. Laubach and von Haeseler developed a java application, TreeSnatcher, which semi-automates the process of extracting Newick-format trees by analyzing the tree structure and branch lengths of pixel images of multifurcating phylogenetic trees. Would be interested to try this one out.

My small palaeobotany collection, courtesy of ebay and its participants, now includes a small fossil cone that I haven't managed to take a good picture of. I'm going to try the digital camera through a 10x microscope, we'll see. Any ideas or pointers for strategies to build an evolutionary sample of fossil plant specimens? The database architect in me sees this as a snowflake schema problem. I'm thinking that age, clade, geographic location, plant part, and accessibilty of sample data are the dominant dimensions. What would be the most informative snowflake sampling strategies? Availability of published trees from the literature, and access to an overall time-based taxonomy would be important.

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De Bodt S, Maere S, Van de Peer Y. (2005). Genome duplication and the origin of angiosperms. Trends in Ecology and Evolution 20:11, 591-597.

Laubach T, von Haeseler A (2007). TreeSnatcher: coding trees from images. Bioinformatics 23, 3384-3385.

McPeek MA, Brown, JM (2007). Clade age and not diversification rate explains species richness among animal taxa. The American Naturalist 169:4, E97-106.

Moore MJ, Bell CD, Soltis PS, Soltis DE (2007). Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms. PNAS 104:49, 19363-19368.