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Aim To introduce and describe the functioning of a new algorithm, phylogenetic analysis for comparing trees (PACT), for generating area cladograms that provide accurate representation of information contained in taxon–area cladograms. Methods PACT operates in the following steps. Convert all phylogenies to taxon–area cladograms. Convert all taxon–area cladograms to Venn diagrams. Choose any taxon–area cladogram from the set of taxon–area cladograms to be analysed and determine its elements. This will be the template area cladogram. Select a second taxon–area cladogram. Determine its elements. Document which elements in the second tree occur in the template tree (denoted by ‘Y’) and which do not (denoted by ‘N’). Each ‘Y’ indicates a match with previous pattern and these are combined. Each ‘N’ is a new element and is attached to the template area cladogram at the node where it is linked with a Y. This requires two rules: (1) ‘Y + Y = Y’ (combine common elements) as long as they are connected at the same node; and (2) ‘Y + N = YN’ (add novel elements to the template area cladogram at the node where they first appear). Once the novel elements in the second taxon–area cladogram have been added to the template area cladogram, see if any of them can be further combined. This requires three additional rules: (1) ‘Y(Y? = Y(Y?’ (do not combine Y's if they are attached at different nodes on the template area cladogram); (2) ‘Y + YN = YN’ (Y is part of group YN); and (3) ‘YN + YN = YNN’ (Y is the same for each, but each N is different). Repeat for all available taxon–area cladograms. Results Three exemplars demonstrate that PACT provides the most accurate area cladograms for vicariance‐driven biotic diversification, dispersal‐driven biotic diversification and taxon pulse‐driven biotic diversification. PACT can also be used as an a priori method of biogeographical analysis. Main conclusions PACT embodies all the strong points and none of the weaknesses of previously proposed methods of historical biogeography. It is most useful as an a posteriori method, but it is also superior to all previous a priori methods because it does not specify costs, or weights or probabilities, or likelihoods of particular biogeographical processes a priori and is thus sensitive to clade‐specific historical contingencies. 相似文献
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Kayce C. Bell Kendall L. Calhoun Eric P. Hoberg John R. Demboski Joseph A. Cook 《Biological journal of the Linnean Society. Linnean Society of London》2016,119(2):397-413
Climate and host demographic cycling often shape both parasite genetic diversity and host distributions, processes that transcend a history of strict host–parasite association. We explored host associations and histories based on an evaluation of mitochondrial and nuclear sequences to reveal the underlying history and genetic structure of a pinworm, Rauschtineria eutamii, infecting ten species of western North American chipmunks (Rodentia:Tamias, subgenus Neotamias). Rauschtineria eutamii contains divergent lineages influenced by the diversity of hosts and variation across the complex topography of western North America. We recovered six reciprocally monophyletic R. eutamii mitochondrial clades, largely supported by a multilocus concordance tree, exhibiting divergence levels comparable with intraspecific variation reported for other nematodes. Phylogenetic relationships among pinworm clades suggest that R. eutamii colonized an ancestral lineage of western chipmunks and lineages persisted during historical isolation in diverging Neotamias species or species groups. Pinworm diversification, however, is incongruent and asynchronous relative to host diversification. Secondarily, patterns of shallow divergence were shaped by geography through events of episodic colonization reflecting an interaction of taxon pulses and ecological fitting among assemblages in recurrent sympatry. Pinworms occasionally infect geographically proximal host species; however, host switching may be unstable or ephemeral, as there is no signal of host switching in the deeper history of R. eutamii. 相似文献
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Aim To present a historical biogeographical protocol for distinguishing biotic diversification by taxon pulse radiations from biotic diversification by vicariance. Location Mexico and northern Central America. Methods Brooks Parsimony Analysis (BPA), phylogenetic inference, linear correlation analysis. Results The taxon pulse radiation of 33 clades in nine areas of endemism in Mesoamerica is based on nine episodes of biotic expansion from three areas, and six episodes of vicariance, involving four geographical splits. Nineteen per cent of speciation events are due to vicariance, 25% to peripheral isolates speciation and 56% are within‐area events. The species–area curve has a correlation coefficient (r2) of 0.47. Extinction events and species richness are highly correlated (r2 = 0.75), but colonization events and species richness are poorly correlated (r2 = 0.36), suggesting that colonization is not the main determinant of the species–area relationship. Colonization events are more poorly correlated with size of area (r2 = 0.05) than are in situ speciation events (r2 = 0.60). Colonization events and in situ events are poorly correlated (r2 = 0.02). All areas of endemism have reticulated histories, and have acted as both sources and islands at various times. Main conclusions Taxon pulses can be distinguished from maximum vicariance using this protocol; refining it requires a method for generating area cladograms from complex data and incorporation of direct dating of evolutionary events. 相似文献
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Mallory E. Eckstut Caleb D. McMahan Brian I. Crother Justin M. Ancheta Deborah A. McLennan Daniel R. Brooks 《Global Ecology and Biogeography》2011,20(4):545-557
Aim To compare the evolutionary and ecological patterns of two extensively studied island biotas with differing geological histories (the Hawaiian Islands and the Greater Antilles). We evaluated the results from PACT (phylogenetic analysis for comparing trees), an innovative approach that has been proposed to reveal general patterns of biotic expansion (between regions) and in situ (within a region) diversification, as well as species–area relationships (SAR) and the taxon pulse dynamic. Location The Hawaiian Islands and Greater Antilles. Methods We used the PACT algorithm to construct general area cladograms and identified biotic expansion and in situ nodes. We analysed the power‐law SAR and relative contribution of biotic expansion and in situ diversification events using power‐law and linear regression analyses. Results Both biotic expansion and in situ nodes were prevalent throughout the PACT general area cladograms (Greater Antilles, 55.9% biotic expansion, 44.1% in situ; Hawaiian Islands, 40.6% biotic expansion, 59.4% in situ). Of the biotic expansion events, both forward and backward events occurred in both regions (Greater Antilles, 85.1% forward, 14.9% backward; Hawaiian Islands, 65% forward, 35% backward). Additionally, there is a power‐law SAR for the Greater Antilles but not for the Hawaiian Islands. However, exclusion of Hawai'i (the youngest, largest Hawaiian Island) produced a power‐law SAR for the Hawaiian Islands. Main conclusions The prevalence of in situ events as well as forward and backward biotic expansion events reveals that both Hawaiian and Greater Antillean biotas have evolved through alternating episodes of biotic expansion and in situ diversification. These patterns are characteristic of the taxon pulse dynamic, for which few data have previously been recorded on islands. Additionally, our analysis revealed that historical influences on the power‐law SARs are pronounced in both assemblages: old, small islands are relatively species rich and young, large islands are relatively species poor. Thus, our PACT results are consistent with hypotheses of geological influence on the evolution of island biotas and also provide greater insight into the role of the taxon pulse dynamic in the formation of island equilibria. 相似文献
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Sophie Picq Fernando Alda Rüdiger Krahe Eldredge Bermingham 《Journal of Biogeography》2014,41(8):1520-1532
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