Trees within trees: phylogeny and historical associations

Page, Roderic; Charleston, Michael A.

doi:10.1016/s0169-5347(98)01438-4

Cited by 271 publications

(257 citation statements)

References 48 publications

(44 reference statements)

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“…So-called 'Jungle' methods, which can estimate the number of horizontal transfer events required to reconcile two incongruent trees (Page & Charleston 1998), may provide one technique for addressing this question. A recent study by Temkin & Eldredge (2007) employed this method and estimated 12 such events in the phylogenetic history of 38 brass instruments over a time period of about 175 years.…”

Section: Discussionmentioning

confidence: 99%

Is horizontal transmission really a problem for phylogenetic comparative methods? A simulation study using continuous cultural traits

Currie

Greenhill

Mace

2010

Phil. Trans. R. Soc. B

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Phylogenetic comparative methods (PCMs) provide a potentially powerful toolkit for testing hypotheses about cultural evolution. Here, we build on previous simulation work to assess the effect horizontal transmission between cultures has on the ability of both phylogenetic and non-phylogenetic methods to make inferences about trait evolution. We found that the mode of horizontal transmission of traits has important consequences for both methods. Where traits were horizontally transmitted separately, PCMs accurately reported when trait evolution was not correlated even at the highest levels of horizontal transmission. By contrast, linear regression analyses often incorrectly concluded that traits were correlated. Where simulated trait evolution was not correlated and traits were horizontally transmitted as a pair, both methods inferred increased levels of positive correlation with increasing horizontal transmission. Where simulated trait evolution was correlated, increasing rates of separate horizontal transmission led to decreasing levels of inferred correlation for both methods, but increasing rates of paired horizontal transmission did not. Furthermore, the PCM was also able to make accurate inferences about the ancestral state of traits. These results suggest that under certain conditions, PCMs can be robust to the effects of horizontal transmission. We discuss ways that future work can investigate the mode and tempo of horizontal transmission of cultural traits.

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Section: Discussionmentioning

confidence: 99%

Is horizontal transmission really a problem for phylogenetic comparative methods? A simulation study using continuous cultural traits

Currie

Greenhill

Mace

2010

Phil. Trans. R. Soc. B

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“…The extinction of a genetic lineage within a species or of a species in a habitat is also classified as a sorting event (e.g. Hafner & Page 1995;Page & Charleston 1998). Sorting can be thought of as the pruning of some branches on the dependent phylogeny, which results in mismatches with the tips of the independent phylogeny.…”

Section: The Cophylogenetic Frameworkmentioning

confidence: 99%

“…In genetics, duplication results in an organism carrying two copies of the same gene. In the case of organism -area associations, duplication is equivalent to sympatric speciation, which occurs within an undivided geographical area or habitat range (Page & Charleston 1998).…”

Section: (C) Duplicationmentioning

confidence: 99%

The cophylogeny of populations and cultures: reconstructing the evolution of Iranian tribal craft traditions using trees and jungles

Tehrani

Collard

Shennan

2010

Phil. Trans. R. Soc. B

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Phylogenetic approaches to culture have shed new light on the role played by population dispersals in the spread and diversification of cultural traditions. However, the fact that cultural inheritance is based on separate mechanisms from genetic inheritance means that socially transmitted traditions have the potential to diverge from population histories. Here, we suggest that associations between these two systems can be reconstructed using techniques developed to study cospeciation between hosts and parasites and related problems in biology. Relationships among the latter are patterned by four main processes: co-divergence, intra-host speciation (duplication), intra-host extinction (sorting) and horizontal transfers. We show that patterns of cultural inheritance are structured by analogous processes, and then demonstrate the applicability of the host-parasite model to culture using empirical data on Iranian tribal populations.

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“…This program uses the reconciled trees approach (Page, 1994) to reconstruct the historical associations between the bird lineages and geographic areas, given a phylogeny for the bird genus and a cladogram representing hypothesized area relationships, with each terminal taxon assigned to an area of endemism as described above (see Table 1). The method maximizes the number of vicariance events (or "co-speciation events" in a host-parasite framework) and permits lineage duplication, but does not accommodate dispersal (Page and Charleston, 1998). The signiWcance of the observed Wt between the bird and area cladograms was evaluated with a randomization test implemented in TreeMap.…”

Section: Biogeographic Analysismentioning

confidence: 99%

Phylogeny and comparative biogeography of Pionopsitta parrots and Pteroglossus toucans

Eberhard

Bermingham

2005

Molecular Phylogenetics and Evolution

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Studies of Neotropical birds, and their distributions and areas of endemism, in particular, have been central in the formulation of hypotheses proposed to explain the high species diversity in the Neotropics. We used mtDNA sequence data (ATPase 6 and 8, COI, and cyt b) to reconstruct the species-level phylogenies for two genera, Pionopsitta (Aves: Psittacidae) and Pteroglossus (Aves: Ramphastidae), compare our results with previous morphology-based phylogenetic analyses, and estimate the absolute timing of lineage and biogeographic divergences. Both the Pionopsitta and Pteroglossus phylogenies support a hypothesis of area relationships in which a divergence of the Serra do Mar (Atlantic Forest, Brazil) region of endemism is followed by the divergence of cis-and transAndean regions, then a split between the upper and lower Amazon basin, next the divergence of the Guyana area, and Wnally diversiWcation of taxa in the upper Amazon basin's areas of endemism. Phylogenies of both genera support a hypothesis of area relationships that is similar to that proposed by Prum [XIX International Ornithological Congress (1988), 2562] for high-vagility species, but while they agree on the relative timing of area divergence (vicariance) events, they yield diVerent absolute time estimates for those divergences when the typical avian mtDNA clock calibration is used. Taken at face value, the time estimates indicate that both genera began to diversify before the start of the Pleistocene, and that climatic and habitat shifts alone do not account for the diversiWcation of these taxa. 

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Trees within trees: phylogeny and historical associations

Cited by 271 publications

References 48 publications

Is horizontal transmission really a problem for phylogenetic comparative methods? A simulation study using continuous cultural traits

Is horizontal transmission really a problem for phylogenetic comparative methods? A simulation study using continuous cultural traits

The cophylogeny of populations and cultures: reconstructing the evolution of Iranian tribal craft traditions using trees and jungles

Phylogeny and comparative biogeography of Pionopsitta parrots and Pteroglossus toucans

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