Assumption 0 Analysis: Comparative Phylogenetic Studies in the Age of Complexity^1,2,3

Abstract

Darwin's panoramic view of biology encompassed two metaphors: the phylogenetic tree, pointing to relatively linear (and divergent) complexity, and the tangled bank, pointing to reticulated (and convergent) complexity. The emergence of phylogenetic systematics half a century ago made it possible to investigate linear complexity in biology. Assumption 0, first proposed in 1986, is not needed for cases of simple evolutionary patterns, but must be invoked when there are complex evolutionary patterns whose hallmark is reticulated relationships. A corollary of Assumption 0, the duplication convention, was proposed in 1990, permitting standard phylogenetic systematic ontology to be used in discovering reticulated evolutionary histories. In 2004, a new algorithm, phylogenetic analysis for comparing trees (PACT), was developed specifically for use in analyses invoking Assumption 0. PACT can help discern complex evolutionary explanations for historical biogeographical, coevolutionary, phylogenetic, and tokogenetic processes.

PACT in practice: comparative historical biogeographic patterns and species-area relationships of the Greater Antillean and Hawaiian Island terrestrial biotas

“…MacArthur & Wilson (1963) did not provide an explicit reason for the confounding effect in in situ speciation events; however, the complication could occur in two ways: (1) if in situ speciation and speciation by colonization are not causally coupled, and (2) if back‐dispersal occurs. In the case of the former, if in situ speciation is a process independent of colonization that may influence the shape of the species–area curve to a considerable extent, depending on the age and size of the island (Heaney, 2000; Halas et al ., 2005; Brooks & van Veller, 2008). In the latter case, back‐dispersal permits islands serving as sinks (‘evolutionary dead ends’) for incoming species to become sources of species to other islands, violating the underlying assumption of a unidirectional source–sink relationship between islands and the ‘mainland’, which is a species source outside the archipelago of concern and may be a continent or another island series.…”

“…Lieberman & Eldredge (1996) presented insights about an alternative process for producing general patterns: geodispersal, where geographic barriers fall and subsequent biotic expansion can produce congruent patterns among clades. Brooks & van Veller (2008) proposed that if non-vicariant mechanisms are a contributing factor to a region's biotic history, then analysis is required where all species and their distributions are analysed without modification, i.e. no branches from the input trees are removed, moved to different nodes or duplicated, so each original input tree can be superimposed in its original form onto the resulting general area cladogram (GAC; see Table 1 for a complete list of abbreviations used in this paper).…”

“…PACT (phylogenetic analysis for comparing trees) is a novel method for biogeographic analysis that builds upon secondary Brooks parsimony analysis (BPA) (Wojcicki & Brooks, 2004, 2005; Brooks & van Veller, 2008) that has previously been used for analysis of species and areas (Folinsbee & Brooks, 2007; Lim, 2008) and also for assessment of historically reticulated and non‐reticulated relationships among parasites and hosts (Brooks & Ferrao, 2005).…”

How specialists can be generalists: resolving the "parasite paradox" and implications for emerging infectious disease

“…Phylogenetic comparative studies of hosts and parasites demonstrate two macroevolutionary patterns: (1) high host specialization and conservatism in host use, as well as (2) abundant evidence of switching onto relatively unrelated hosts that in some cases seems to have been the primary driver of diversification (AGOSTA 2006, JANZ et al 2006, JANZ & NYLIN 2008, WINKLER & MITTER 2008, NYMAN 2009). As a corollary, objective evidence for cospeciation has been rare even among intimately associated parasites, such as helminths inhabiting vertebrates (BROOKS & MCLENNAN 1991, BROOKS et al 2006b, BROOKS & VAN VELLER 2008, 2010. For less intimate associations, such as among plants and many plant-feeding insects, it has long been recognized that cospeciation cannot have been a major source of diversification (AGOSTA 2006, NYMAN 2009.…”

Biogeography of Amazonian fishes: deconstructing river basins as biogeographic units

“…No specific treatment was applied to redundant distributions (areas with more than one taxon in the cladogram). Assumption A0 guided the interpretation for widespread taxa in all analyses (Van Veller et al, 2000Brooks, Van Veller, 2008) i.e., shared presence of a species is regarded as evidence of common origin -incidentally one of the most contentious elements in biogeographic methods. Lineages restricted to only one basin (autapomorphic taxa or clade), albeit uninformative about area relationships, were not excluded so that the matrix is fully reflective of the database, including information on endemic taxa for each drainage (S7-10 -Available only as online supplementary file accessed with the online version of the article at http://www.scielo.br/ni).…”