title: Testing for adaptive evolution of the female reproductive protein ZPC in mammals, birds and fishes reveals problems with the M7-M8 likelihood ratio test.
abstract: BACKGROUND
  Adaptive evolution appears to be a common feature of reproductive proteins across a very wide range of organisms. A promising way of addressing the evolutionary forces responsible for this general phenomenon is to test for adaptive evolution in the same gene but among groups of species, which differ in their reproductive biology. One can then test evolutionary hypotheses by asking whether the variation in adaptive evolution is consistent with the variation in reproductive biology. We have attempted to apply this approach to the study of a female reproductive protein, zona pellucida C (ZPC), which has been previously shown by the use of likelihood ratio tests (LRTs) to be under positive selection in mammals.
  
  
  RESULTS
  We tested for evidence of adaptive evolution of ZPC in 15 mammalian species, in 11 avian species and in six fish species using three different LRTs (M1a-M2a, M7-M8, and M8a-M8). The only significant findings of adaptive evolution came from the M7-M8 test in mammals and fishes. Since LRTs of adaptive evolution may yield false positives in some situations, we examined the properties of the LRTs by several different simulation methods. When we simulated data to test the robustness of the LRTs, we found that the pattern of evolution in ZPC generates an excess of false positives for the M7-M8 LRT but not for the M1a-M2a or M8a-M8 LRTs. This bias is strong enough to have generated the significant M7-M8 results for mammals and fishes.
  
  
  CONCLUSIONS
  We conclude that there is no strong evidence for adaptive evolution of ZPC in any of the vertebrate groups we studied, and that the M7-M8 LRT can be biased towards false inference of adaptive evolution by certain patterns of non-adaptive evolution.
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18 D, 752 36 Uppsala, Sweden. sofia.berlin@bbsrc.ac.uk
authors.forename: Sofia
authors.initials: S
authors.lastname: Berlin
authors.forename: Nick G C
authors.initials: NG
authors.lastname: Smith
mesh_terms: D000220:Adaptation, Biological; D000818:Animals; D005075:Biological Evolution; D001717:Birds; D003062:Codon; D003198:Computer Simulation; D019143:Evolution, Molecular; D005260:Female; D005399:Fishes; D016013:Likelihood Functions; D008322:Mammals; D008562:Membrane Glycoproteins / Q000378:metabolism / Q000502:physiology*; D008954:Models, Biological; D008957:Models, Genetic; D010802:Phylogeny; D011110:Polymorphism, Genetic; D012107:Research Design; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D015027:Zebrafish; D029961:Zebrafish Proteins / Q000378:metabolism / Q000502:physiology*
chemical_list: D003062:Codon; D008562:Membrane Glycoproteins; D029961:Zebrafish Proteins; C487635:zp3b protein, zebrafish