Evolution, Theory of physiology and morphology, evolutionary systematic biology, evolutionary genetics, molecular evolution, and human evolution Research in all of these fields, and the interdisciplinary overlaps between them, have accelerated in the past 30 years Two areas of explosive research deserve special mention First, the field of molecular evolution, from being scarcely existent in 1950, has become a burgeoning field comprising a large part of the research program of evolutionary biology (Higgs and Attwood, 2005; Edwards, 2009) It was realized early on that, once available, molecular sequence data, of either amino acids or DNA, would be ‘‘documents of evolutionary history’’ (Zuckerkandl and Pauling, 1965) and that branching sequences, ancestral states, and rates of evolution could be estimated from such data This realization has proven abundantly true, and molecular data now form the basis of the phylogenetic estimates for large swaths of the tree of life (Felsenstein, 2004; Hall, 2011; Hillis, 2010) Molecular data have contributed to the understanding of not only evolutionary history but also evolutionary mechanisms In the 1960s, protein electrophoresis revealed high levels of genetic variation in natural populations, which answered old questions about the amounts of natural genetic variation and posed new ones about the maintenance of variation (Lewontin, 1974) The advent of DNA sequencing has revolutionized evolutionary molecular genetics (Kreitman, 1983), and such data now allow hypotheses about the relative importance of drift and selection on particular loci and regions to be effectively tested (Charlesworth and Charlesworth, 2010) As well, the sequencing of whole genomes of an ever-expanding variety of organisms has led to the emergence of comparative genomics, in which entire genomic structures can be compared, and their evolutionary histories and the forces shaping them studied (Lynch, 2007; Edwards, 2009) The second is the field of evolutionary developmental biology, or ‘‘evo devo’’ as it is known, another field that scarcely existed in 1950 It too has become a vibrant research program, focused on the study of the developmental pathways by which organismal features are produced, the genetic basis of alterations in these pathways that are evolutionarily incorporated within lineages, and the biases or constraints that may be imposed on phenotypic evolution by these alterations Most of evolution is the modification of preexisting structures, and these structures arise in the organism via a process of epigenetic (in the original sense: Haig, 2004) development Thus, most of evolution is the modification of preexisting developmental programs To understand phenotypic evolution, one must understand the variations that alterations of the developmental program can give rise to, their natures, and frequency, and these studies are the domain of evo devo (Carroll, 2005; Carroll et al., 2005; True, 2009; Wray, 2010; Stern, 2011) One of the most exciting developments in this field has been the discovery of a number of developmental regulatory genes, such as Hox genes, that regulate the spatial expression of genes in developing animal embryos, and which are conserved among taxa as disparate as arthropods and vertebrates The two major groups of bilaterian animals – the protosomes (Ecdysozoa and Lophotrochozoa) and the deuterostomes (Chordata and Echinodermata) – share a common genetic regulatory repertoire and are characterized by an extensive 395 cluster of Hox genes that bind to DNA and control interacting networks of developmental regulators and key structural genes (Knoll and Carroll, 1999) (Figure 2) This repertoire of genes, which was present in the common ancestor of the Bilateria, has been referred to as a ‘‘genetic toolkit’’ for the development and evolution of basic animal morphologies, and understanding their action and evolution will aid in understanding such features as germ layers, coelom formation, and spatial organization (Carroll et al., 2005) Darwin’s Five Theories Although Darwin often used expressions such as ‘‘my theory,’’ he actually proposed a number of distinct, though related, theories Some, such as his theory of inheritance, termed ‘‘pangenesis,’’ were wrong and are of historical interest only But a cluster of other theories has been borne out by subsequent developments in evolutionary biology, and it is useful to consider these ideas here Mayr (1991, 2001) has identified a set of these ideas as ‘‘Darwin’s five theories,’’ and his usage has been followed and adapted by later authors (Futuyma, 1998, 2009; Coyne, 2009), and the following account is adapted from this approach The first is evolution as such, the simple idea that later organisms are the modified descendants of earlier organisms This idea had also been advocated by Lamarck Darwin convinced essentially all of his scientific contemporaries of the truth of this proposition The evidence for this may be found in any evolution textbook (e.g., Freeman and Herron, 2007; Hall and Hallgrimsson, 2008; Futuyma, 2009), and in more popular expositions by Coyne (2009) and Dawkins (2009) The second is common ancestry, which had been rejected by nontransformists such as Cuvier, who held that the four ‘‘embranchements’’ of animal life (Vertebrata, Radiata, Articulata, and Mollusc) were so essentially different that they could not be connected by any possible transformation (Young, 2007) Common ancestry may seem to follow from evolution as such, but it does not: Lamarck, it will be recalled, proposed continual spontaneous generation, with each origination progressing up the chain of being, and thus not being genealogically related to earlier or later originations Darwin (1859, p 490) proposed that life had been ‘‘breathed into a few forms or into one,’’ and thus most or all organic beings would be connected by a single tree of life This contention has been abundantly borne out by phylogenetic studies within eukaryotes, but the eukaryotes appear to be chimeric in their origin, incorporating by lateral or horizontal gene transfer both Archaebacterial and/or Eubacterial genes in their nuclear and organellar genomes A phylogenetic tree based on small subunit RNA places the eukaryotes as sister to the Archaebacteria (Knoll, 2003), but large-scale genomic analyses are in disagreement about the nature, extent, and phylogenetic significance of the shared genomic components Although some whole genome incorporation via endosymbiosis (e.g., mitochondria) is well established, the possibility of extensive lateral transfer of genes among prokaryotes and early eukaryotes has led Lynch (2007) to ask if life is a tree, ring, or web; resolution of the relationship among the domains of life remains a major task for phylogenetics (Gribaldo et al., 2010) (Figure 3)