Reweaving the Tapestry: What Can We Learn from Sibley and Ahlquist (1990)?

Abstract

ABsTRAcr.-Sibley and Ahlquist's phylogeny of the birds (The Tapestry) has drawn both praise and criticism. Two major criticisms are that trees were based on incomplete distance matrices and that their tree-building algorithm (UPGMA) was inappropriate. Their 1990 book answered critics by including several complete matrices analyzed by the Fitch-Margoliash algorithm. Matrices were constructed by combining species into composite taxa, which requires additional (possibly defensible) assumptions and introduces additional (probably random) error. Three problems remain: (1) The algorithm used does not always find the bestfit topology, depending on taxon order. (2) The error variance of the data does not fit the assumptions of the Fitch-Margoliash algorithm. The assumptions of the algorithms of Fitch and Margoliash and of Cavalli-Sforza and Edwards are limiting cases that bracket the truth. (3) Even a matrix with no phylogenetic content has a best-fit topology; some test of the strength of support for branches on a tree is required. To address these problems, I analyzed: (1) each matrix several times with different orderings of taxa and with user-defined trees; (2) each matrix with both algorithms; (3) upper-right and lower-left halves of each matrix separately, performed a complete set of single-taxon jackknifings, and created a jackknife strict consensus of all best-fit trees using both algorithms. Based on these analyses, 97 of 173 interior branches (56%) on the FITCH trees published by Sibley and Ahlquist (1990) were still present in my consensus trees. Many trees remained nearly intact; others collapsed into polytomies. I found that 11 of 97 remaining branches (11%) contradict the Tapestry. I conclude that the data in Sibley and Ahlquist (1990), properly analyzed, have a strong phylogenetic signal.