We explore the evidential relationships that connect two standard claims of modern evolutionary biology. The hypothesis of common ancestry (which says that all organisms now on earth trace back to a single progenitor) and the hypothesis of natural selection (which says that natural selection has been an important influence on the traits exhibited by organisms) are logically independent; however, this leaves open whether testing one requires assumptions about the status of the other. Darwin noted that an extreme version of adaptationism (...) would undercut the possibility of making inferences about common ancestry. Here we develop a converse claim—hypotheses that assert that natural selection has been an important influence on trait values are untestable unless supplemented by suitable background assumptions. The fact of common ancestry and a claim about quantitative genetics together suffice to render such hypotheses testable. Furthermore, we see no plausible alternative to these assumptions; we hypothesize that they are necessary as well as sufficient for adaptive hypotheses to be tested. This point has important implications for biological practice, since biologists standardly assume that adaptive hypotheses predict trait associations among tip species. Another consequence is that adaptive hypotheses cannot be confirmed or disconfirmed by a trait value that is universal within a single species, if that trait value deviates even slightly from the optimum. 1 Two Darwinian hypotheses 2 Logical independence 3 How adaptive hypotheses bear on the tree of life hypothesis 4 How the tree of life hypothesis bears on adaptive hypotheses 5 What do adaptive hypotheses predict? 6 Common ancestry and quantitative genetics to the rescue 7 Conclusion. (shrink)

FEW HEROES LOWER their sights in the prime of their lives; triumph leads inexorably on, often to destruction. Alexander wept because he had no new worlds to conquer; Napoleon, overextended, sealed his doom in the depth of a Russian winter. But Charles Darwin did not follow the Origin of Species (1859) with a general defense of natural selection or with its evident extension to human evolution (he waited until 1871 to publish The Descent of Man). Instead, he wrote his most (...) obscure work, a book entitled: On the Various Contrivances by Which British and Foreign Orchids Are Fertilized by Insects (1862). (shrink)

Although the justification for using cladistic parsimony to infer phylogenetic trees has been extensively discussed, much less attention has been paid to the use of cladistic parsimony to reconstruct the character states of the ancestral species postulated by an inferred phylogenetic tree. These two problems differ in terms of both their inputs and their outputs, as shown in the following table. In the former, one begins with data on the character states of extant species and tries to find the best (...) supported phylogenetic tree. In the latter, one begins with the tree that is most firmly supported by characteristics C1, C2,... Cn-1; one then takes some new characteristic Cn and records the character states of Cn that attach to the tree’s interior nodes, which represent common ancestors. In both cases, cladistic parsimony solves the problem by finding the hypothesis that requires the fewest changes in character state that are needed to explain the observations. (shrink)

This paper investigates the possibility of extending the likelihood treatment of support to situations in which the evidence and the hypotheses supported by the evidence are all outcomes of a chance process. An example is when we ask how much support the observed sequence of heads and tails gives to the hypothesis that the next toss will be a head. I begin by discussing Sober’s approach to a problem of this type: that of estimating how much support the observation that (...) I have a mind gives to the hypothesis that you do. I criticize his approach, and offer a general solution to the problem. (shrink)