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2.  Darwin would have loved DNA: celebrating Darwin 200 
Biology Letters  2009;5(4):503-505.
Analysis of DNA sequences now plays a key role in evolutionary biology research. If Darwin were to come back today, I think he would be absolutely delighted with molecular evolutionary genetics, for three reasons. First, it solved one of the greatest problems for his theory of evolution by natural selection. Second, it gives us a tool that can be used to investigate many of the questions he found the most fascinating. And third, DNA data confirm Darwin's grand view of evolution.
doi:10.1098/rsbl.2009.0298
PMCID: PMC2781938  PMID: 19447813
molecular evolution; heredity; macroevolution; pangenesis; gemmule; central dogma
3.  Why do species vary in their rate of molecular evolution? 
Biology Letters  2009;5(3):401-404.
Despite hopes that the processes of molecular evolution would be simple, clock-like and essentially universal, variation in the rate of molecular evolution is manifest at all levels of biological organization. Furthermore, it has become clear that rate variation has a systematic component: rate of molecular evolution can vary consistently with species body size, population dynamics, lifestyle and location. This suggests that the rate of molecular evolution should be considered part of life-history variation between species, which must be taken into account when interpreting DNA sequence differences between lineages. Uncovering the causes and correlates of rate variation may allow the development of new biologically motivated models of molecular evolution that may improve bioinformatic and phylogenetic analyses.
doi:10.1098/rsbl.2009.0136
PMCID: PMC2679939  PMID: 19364710
molecular clock; phylogenetics; dating; mutation; substitution; population size
4.  Putting the ‘bio’ into bioinformatics 
Biology Letters  2009;5(3):391-393.
Bioinformatic analyses have grown rapidly in sophistication and efficiency to accommodate the vast increase in available data. One of the major challenges has been to incorporate the growing appreciation of the complexity of molecular evolution into new analytical methods. As the reliance on molecular data in biology and medicine increases, we need to be confident that these methods adequately reflect the underlying processes of genome change. This special issue focuses on the way that patterns and processes of molecular evolution are influenced by features of populations of whole organisms, such as selection pressure, population size and life history. The advantage of this approach to molecular evolution is that it views genomic change not simply as a biochemical or stochastic process, but as the result of a complex series of interactions that shape the kinds of genomic changes that can and do happen.
doi:10.1098/rsbl.2009.0227
PMCID: PMC2679943  PMID: 19386649
mutation; substitution; molecular evolution; relaxed clocks; barcoding; alignment
5.  Primates follow the ‘island rule’: implications for interpreting Homo floresiensis 
Biology Letters  2007;3(4):398-400.
When the diminutive skeleton of Homo floresiensis was found on the Indonesian island of Flores, it was interpreted as an island dwarf, conforming to the ‘island rule’ that large animals evolve smaller size on islands, but small animals tend to get larger. However, previous studies of the island rule have not included primates, so the extent to which insular primate populations undergo size change was unknown. We use a comparative database of 39 independently derived island endemic primate species and subspecies to demonstrate that primates do conform to the island rule: small-bodied primates tend to get larger on islands, and large-bodied primates get smaller. Furthermore, larger species undergo a proportionally greater reduction in size on islands.
doi:10.1098/rsbl.2007.0113
PMCID: PMC2390661  PMID: 17439845
insular dwarf; comparative method; Homo floresiensis

Results 1-5 (5)