title: Statistical evidence for common ancestry: Application to primates.
abstract: Since Darwin, biologists have come to recognize that the theory of descent from common ancestry (CA) is very well supported by diverse lines of evidence. However, while the qualitative evidence is overwhelming, we also need formal methods for quantifying the evidential support for CA over the alternative hypothesis of separate ancestry (SA). In this article, we explore a diversity of statistical methods using data from the primates. We focus on two alternatives to CA, species SA (the separate origin of each named species) and family SA (the separate origin of each family). We implemented statistical tests based on morphological, molecular, and biogeographic data and developed two new methods: one that tests for phylogenetic autocorrelation while correcting for variation due to confounding ecological traits and a method for examining whether fossil taxa have fewer derived differences than living taxa. We overwhelmingly rejected both species and family SA with infinitesimal P values. We compare these results with those from two companion papers, which also found tremendously strong support for the CA of all primates, and discuss future directions and general philosophical issues that pertain to statistical testing of historical hypotheses such as CA.
authors.affiliation: Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, Wisconsin, 53706. dbaum@wisc.edu.
authors.forename: David A
authors.initials: DA
authors.lastname: Baum
authors.affiliation: Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, Wisconsin, 53706.|Department of Statistics, University of Wisconsin, 1300 University Avenue, Madison, Wisconsin, 53706.
authors.forename: Cécile
authors.initials: C
authors.lastname: Ané
authors.affiliation: Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, Wisconsin, 53706.|Department of Statistics, University of Wisconsin, 1300 University Avenue, Madison, Wisconsin, 53706.
authors.forename: Bret
authors.initials: B
authors.lastname: Larget
authors.affiliation: Department of Statistics, University of Wisconsin, 1300 University Avenue, Madison, Wisconsin, 53706.
authors.forename: Claudia
authors.initials: C
authors.lastname: Solís-Lemus
authors.affiliation: Department of Statistics, University of Wisconsin, 1300 University Avenue, Madison, Wisconsin, 53706.
authors.forename: Lam Si Tung
authors.initials: LS
authors.lastname: Ho
authors.affiliation: Department of Zoology, University of Wisconsin, 250 N. Mills St., Madison, Wisconsin, 53706.
authors.forename: Peggy
authors.initials: P
authors.lastname: Boone
authors.affiliation: Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, Wisconsin, 53706.
authors.forename: Chloe P
authors.initials: CP
authors.lastname: Drummond
authors.affiliation: 5Laboratory of Genetics, University of Wisconsin, 425 Henry Mall, Madison, Wisconsin, 53706.
authors.forename: Martin
authors.initials: M
authors.lastname: Bontrager
authors.affiliation: Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, Wisconsin, 53706.
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Hunter
authors.affiliation: Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, Wisconsin, 53706.
authors.forename: William
authors.initials: W
authors.lastname: Saucier
mesh_terms: D063147:Animal Distribution; D000818:Animals; D005075:Biological Evolution; D002965:Classification / Q000379:methods*; D005580:Fossils / Q000033:anatomy & histology; D008957:Models, Genetic; D015233:Models, Statistical; D010802:Phylogeny; D011323:Primates / Q000033:anatomy & histology / Q000145:classification* / Q000235:genetics / Q000502:physiology
keywords: Biogeography; fossils; permutation tail probability; phylogenetic autocorrelation; separate ancestry; tree agreement