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United States Department of Agriculture

Agricultural Research Service

Title: Ending a Decade of Deception: a Valiant Failure, a Not-So-Valiant Failure, and a Success Story

Authors
item Brooks, Daniel - DEPT ZOOLOGY CANADA
item Dowling, Ashley - U MICHIGAN ANN ARBOR MI
item Van Veller, Marco - THE NETHERLANDS
item Hoberg, Eric

Submitted to: Cladistics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 24, 2003
Publication Date: January 17, 2004
Citation: Brooks, D.R., Dowling, A.P., Van Veller, M.G., Hoberg, E.P. 2004. Ending a decade of deception: a valiant failure, a not-so-valiant failure, and a success story. Cladistics. 20:32-46.

Interpretive Summary: Studies of coevolution and biogeography (geographic distributions) are at the core of understanding the evolution of complex biological systems represented by associations of hosts and parasites. Brooks Parsimony Analysis (BPA) and TreeMap (TM) represent competing methods for studying the history of host associations and the distributions of both hosts and parasites. BPA is an analytical tool designed to search for the intricate connections that determine the structure of host-parasite systems, and specifically to reveal instances of coevolution, colonization (host-switching) and extinction; BPA does not rely on formal assumptions about the structure of such systems. In contrast, TM is dependant upon formal assumptions about the role of cospeciation, and is designed to maximize recognition of instances of this component of coevolution in the study of host-parasite assemblages. Prior studies involving the two methods, Brooks Parsimony Analysis and TreeMap, have found BPA to be the more reliable method. Recent criticisms leveled at these studies argue that the tests were unfairly created and biased in favor of BPA. The authors of a recent critique offer new exemplars to show flaws in BPA plus a simple fix to correct flaws found in TreeMap. Reevaluation of their exemplars clearly shows that the authors' calculations are incorrect. Furthermore, the exemplars by these authors corroborate previous findings that BPA, when calculated correctly, is more reliable than TreeMap1.0 and TreeMap 2.02 and therefore the method of choice in coevolutionary and biogeographical studies. BPA provides an important cornerstone in examining the history of parasites and pathogens in both domestic and wild hosts, and has been applied to studies of primary helminthes in ruminants.

Technical Abstract: Prior studies involving two methods, Brooks Parsimony Analysis and TreeMap, have found BPA to be the more reliable method. Recent criticisms leveled at these studies argue that the tests were unfairly created and biased in favor of BPA. The authors of a recent critique offer new exemplars to show flaws in BPA plus a simple fix to correct flaws found in TreeMap. Reevaluation of their exemplars clearly shows that the authors' calculations are incorrect, their understanding of the methods is lacking, and that their simple fix does not work. Additional analyses using TreeMap 2.02 are run to show that the TreeMap 2.02, like TreeMap 1.0, cannot adequately deal with widespread parasites, contrary to the claims of its supporters. Furthermore, the exemplars corroborate previous findings that BPA, when calculated correctly, is more reliable than TreeMap1.0 and TreeMap 2.02 and therefore the method of choice in coevolutionary and biogeographical studies.

Last Modified: 11/25/2014
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