Phylogeny Reconstruction: The Role of Morphology

Scotland, Robert W.; Olmstead, Richard G.; Bennett, Jonathan

doi:10.1080/10635150309309

Cited by 256 publications

(281 citation statements)

References 90 publications

(159 reference statements)

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“…The theoretical ideal might be to score the fossil and extant taxa for morphological characters, and infer the placement of the fossil taxa from a morphological (Crepet & Herendeen 1992) or simultaneous morphological-molecular phylogenetic analysis. Problems with this are the limited phylogenetic resolution often obtainable from morphological characters (Scotland et al 2003), and missing data for fossils in a simultaneous analysis because their DNA cannot be sequenced. This may cause their position in the resulting phylogenetic trees to be unstable (Platnick et al 1991).…”

Section: Conclusion: Ways Forwardmentioning

confidence: 99%

Introduction and synthesis: plant phylogeny and the origin of major biomes

Pennington

Cronk

Richardson³

2004

Phil. Trans. R. Soc. Lond. B

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Phylogenetic trees based upon DNA sequence data, when calibrated with a dimension of time, allow inference of: (i) the pattern of accumulation of lineages through time; (ii) the time of origin of monophyletic groups; (iii) when lineages arrived in different geographical areas; (iv) the time of origin of biome-specific morphologies. This gives a powerful new view of the history of biomes that in many cases is not provided by the incomplete plant fossil record. Dated plant phylogenies for angiosperm families such as Leguminosae (Fabaceae), Melastomataceae sensu stricto, Annonaceae and Rhamnaceae indicate that long-distance, transoceanic dispersal has played an important role in shaping their distributions, and that this can obscure any effect of tectonic history, previously assumed to have been the major cause of their biogeographic patterns. Dispersal from other continents has also been i mportant in the assembly of the Amazonian rainforest flora and the Australian flora. Comparison of dated biogeographic patterns of plants and animals suggests that recent long-distance dispersal might be more prevalent in plants, which has major implications for community assembly and coevolution. Dated plant phylogenies also reveal the role of past environmental changes on the evolution of lineages in species-rich biomes, and show that recent Plio-Pleistocene diversification has contributed substantially to their current species richness. Because of the critical role of fossils and morphological characters in assigning ages to nodes in phylogenetic trees, future studies must include careful morphological consideration of fossils and their extant relatives in a phylogenetic context. Ideal study systems will be based upon DNA sequence data from multiple loci and multiple fossil calibrations. This allows cross-validation both of age estimates from different loci, and from different fossil calibrations. For a more complete view of biome history, future studies should emphasize full taxon sampling in ecologically important groups, and should focus on geographical areas for which few species-level phylogenies are available, such as tropical Africa and Asia. These studies are urgent because understanding the history of biomes can both inform conservation decisions, and help predict the effects of future environmental changes at a time when biodiversity is being impacted on an unprecedented scale.

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Section: Conclusion: Ways Forwardmentioning

confidence: 99%

Introduction and synthesis: plant phylogeny and the origin of major biomes

Pennington

Cronk

Richardson³

2004

Phil. Trans. R. Soc. Lond. B

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“…31) and gross generalizations on the value of morphology (e.g., ref. 32), this issue has yet to be addressed quantitatively. Here, we evaluate the phylogenetic status of morphogenera relative to molecular phylogenies in 2 paleobiologically and ecologically important clades, Mammalia and Mollusca, and assess the potential impact of incorrect assumption of generic monophyly on 2 key macroevolutionary and macroecological variables: body size (9,(33)(34)(35) and latitudinal range (36)(37)(38)(39)(40)(41).…”

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confidence: 99%

Congruence of morphologically-defined genera with molecular phylogenies

Jablonski

Finarelli

2009

Proc. Natl. Acad. Sci. U.S.A.

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Morphologically-defined mammalian and molluscan genera (herein ''morphogenera'') are significantly more likely to be monophyletic relative to molecular phylogenies than random, under 3 different models of expected monophyly rates: Ϸ63% of 425 surveyed morphogenera are monophyletic and 19% are polyphyletic, although certain groups appear to be problematic (e.g., nonmarine, unionoid bivalves). Compiled nonmonophyly rates are probably extreme values, because molecular analyses have focused on ''problem'' taxa, and molecular topologies (treated herein as error-free) contain contradictory groupings across analyses for 10% of molluscan morphogenera and 37% of mammalian morphogenera. Both body size and geographic range, 2 key macroevolutionary and macroecological variables, show significant rank correlations between values for morphogenera and molecularlydefined clades, even when strictly monophyletic morphogenera are excluded from analyses. Thus, although morphogenera can be imperfect reflections of phylogeny, large-scale statistical treatments of diversity dynamics or macroevolutionary variables in time and space are unlikely to be misleading.biogeography ͉ body size ͉ macroecology ͉ macroevolution ͉ systematics M orphologically-defined genera are the primary analytical units for a wide range of large-scale paleontological and neontological analyses, across topics such as global diversity dynamics (1-8), macroevolutionary trends (9-11), paleoecology (12-14), systematics (15, 16), biogeography (17-19), and conservation biology (20-23). Although assigning rank to sets of species sharing close morphological affinities (usually with 1 or more diagnostic characters) lacks rigorous criteria, analyses of genus-level operational units are less subject to sampling and other biases than species-level analyses (24-26) and generally capture a damped record of species-level patterns (4, 27, 28). However, the proliferation of phylogenetic analyses using molecular data has uncovered an increasing number of paraphyletic or polyphyletic morphogenera (e.g., refs. 29 and 30), calling into question their analytic utility. Yet, despite alarming cases (e.g., ref. 31) and gross generalizations on the value of morphology (e.g., ref. 32), this issue has yet to be addressed quantitatively. Here, we evaluate the phylogenetic status of morphogenera relative to molecular phylogenies in 2 paleobiologically and ecologically important clades, Mammalia and Mollusca, and assess the potential impact of incorrect assumption of generic monophyly on 2 key macroevolutionary and macroecological variables: body size (9, 33-35) and latitudinal range (36-41). ResultsRates of Paraphyly and Polyphyly. We coded each of the 425 genera in our database (Table S1) as monophyletic, paraphyletic, or polyphyletic (42) (Fig. 1). The probability of randomly drawing a cladogram consistent with monophyly for a particular morphogenus from the set of all potential cladograms varies with the number of species in each analysis and in each morphogenus, but does not exceed 4.7% ...

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“…This combination improves the resolution, internal support and overall quality of phylogenetic studies (Caddick et al 2002;Scotland et al 2003). In many instances, there exists a lack of either morphological or molecular data (Giribet et al 2001).…”

Section: Discussionmentioning

confidence: 99%