What Does Palaeontology Contribute to Systematics in a Molecular World?

Smith, Andrew B.

doi:10.1006/mpev.1998.0488

Cited by 54 publications

(57 citation statements)

References 49 publications

(56 reference statements)

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“…rates of diversification) or historical determinants of diversification, as geologically induced vicariance. Fossil data (e.g., Fleischer et al, 1998) and biogeographic events (e.g., García-Moreno and Mindell, 2000) can be used as calibration points for estimating molecular divergence times (Smith, 1998). However, for Ramphastidae, this information is very scarce (Feduccia, 1996;Sick, 1993).…”

Section: Discussionmentioning

confidence: 99%

Diversification of Ramphastinae (Aves, Ramphastidae) prior to the Cretaceous/Tertiary boundary as shown by molecular clock of mtDNA sequences

et al. 2003

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Partial cytochrome b and 12S rDNA mitochondrial DNA sequences of eight representatives of the Ramphastidae family were analyzed. We applied the linearized tree method to identify sequences evolving at similar rates and estimated the divergence times among some of the taxa analyzed. After excluding Ramphastos tucanus and Capito dayi from our data set, the remaining taxa presented a constant rate of DNA substitution, and branch lengths could be re-estimated with a clock constraint using the maximum likelihood method. Branch lengths were calibrated assuming that Galliformes and Piciformes split around 100 million years ago (mya). Our results indicate that Ramphastinae, and probably Capitoninae, diverged from other Piciformes in the Late Cretaceous (~82 mya), suggesting that Piciformes is another avian order that survived the mass extinction event occurred 65 mya at the Cretaceous/Tertiary (K/T) boundary. The divergence times estimated within the Ramphastinae genera cover the period from the Middle Eocene (around 47 mya) through the Late Miocene (9.5 mya). Our estimate of divergence time is coincidental with the split of the African and the South American continents and other intense geologic activities and modifications of the areas which correspond to the current Neotropics. These events might have influenced the diversification of Ramphastinae in South America.

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Section: Discussionmentioning

confidence: 99%

Diversification of Ramphastinae (Aves, Ramphastidae) prior to the Cretaceous/Tertiary boundary as shown by molecular clock of mtDNA sequences

et al. 2003

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“…Smith (1998:440) discussed several examples of increasing taxon sampling in the context of fossil taxa and concluded that "the addition of fossil taxa to a primary matrix has a similar beneficial effect as adding more characters." Smith (1998) cited the contributions of Doyle and Donoghue (1987) and Donoghue et al (1989) for first pointing out the beneficial effect of dense sampling in the context of fossils. Doyle and Donoghue (1987) argued that increased sampling of fossil taxa was crucial for an accurate understanding of phylogeny and character evolution.…”

Section: More Morphological Characters or Fewer?mentioning

confidence: 99%

“…However, in the context of recent molecular analyses (Mathews and Donoghue, 1999;Qiu et al, 1999;Soltis et al, 1999;Barkman et al, 2000;Bowe et al, 2000;Chaw et al, 2000;Graham and Olmstead, 2000), earlier studies based on morphological data and dense sampling of fossils (Crane, 1985;Doyle and Donoghue, 1986, 1987, 1992Loconte and Stevenson, 1990;Nixon et al, 1994) have now been recognized as being inaccurate estimates of phylogeny (Doyle and Endress, 2000). Therefore, although it can be demonstrated that adding taxa with unique combinations of characters can alter a topology (Doyle and Donoghue, 1987;Smith, 1994Smith, , 1998 and sometimes give slightly increased levels of support (Lecointre et al, 1993;Baker et al, 1998;Smith, 1998), this is not the same as increasing the accuracy of a given estimate. It is unclear whether breaking up long branches by dense taxon sampling (Gauthier et al, 1988;Graybeal, 1998) using morphological data on the basis of reduced cost or specimen accessibility (Hillis and Wiens, 2000) will lead to a more accurate assessment of phylogeny.…”

Section: More Morphological Characters or Fewer?mentioning

confidence: 99%

“…It is unclear whether breaking up long branches by dense taxon sampling (Gauthier et al, 1988;Graybeal, 1998) using morphological data on the basis of reduced cost or specimen accessibility (Hillis and Wiens, 2000) will lead to a more accurate assessment of phylogeny. Morphological data from fossil taxa can increase taxon sampling in a way not possible for sequence data, and therefore these data can potentially provide unique character combinations and information on polarity and can alter ideas on character evolution, rooting, and homology assessment (Patterson, 1981;Doyle and Donoghue, 1987;Gauthier et al, 1988;Huelsenbeck, 1991;Smith, 1994Smith, , 1998Benton, 1998). What remains unclear is whether this potential is realized in the context of accurate phylogeny reconstruction, given that these data will suffer from problems discussed above (Figs.…”

Section: More Morphological Characters or Fewer?mentioning

confidence: 99%

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Phylogeny Reconstruction: The Role of Morphology

Scotland¹,

Olmstead²,

Bennett³

2003

Systematic Biology

269

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In this article we explore the paradox of why morphological data are currently utilized less for phylogeny reconstruction than are DNA sequence data, whereas most of what we know about phylogeny stems from classifications founded on morphological data. The crucial difference between the two data sources relates to the number of potentially unambiguous characters available, their ease and speed of discovery, and their suitability for analysis using transformational models. We consider that the increased use of DNA sequence data, relative to morphology, for phylogeny reconstruction is inevitable and well founded, but that a crucial issue remains concerning the role of morphology in phylogeny reconstruction. We present the view that rigorous and critical anatomical studies of fewer morphological characters, in the context of molecular phylogenies, is a more fruitful approach to integrating the strengths of morphological data with those of sequence data. This approach is preferable to compiling larger data matrices of increasingly ambiguous and problematic morphological characters.We argue below that a main constraint of morphologybased phylogenetic inference concerns the limited number of unambiguous characters available for analysis in a transformational framework. This problem of a limited number of unambiguous characters is further compounded by obstacles to accurate homology assessment and character coding, which further reduce the number of characters available for analysis. We discuss and disagree with the view that more morphological data should be used in phylogeny reconstruction. Furthermore, we consider the claim that the greatest strength of morphological data-increased taxon sampling-to be mistaken. In the discussion that follows we use "phylogeny reconstruction" to refer to the computer-based algorithmic analyses routinely conducted in systematics today. NUMBERS OF CHARACTERS Accuracy and SupportHillis (1987) cited the increased number of characters as the greatest advantage of molecular data. Increased numbers of characters have been shown to be crucial in relation to issues of accuracy (Hillis, 1987(Hillis, , 1996(Hillis, , 1998Huelsenbeck and Hillis, 1993;Hillis et al., 1994aHillis et al., , 1994bLamboy, 1994;Cummings et al., 1995;Givnish and Sytsma, 1997b;Rosenberg and Kumar, 2001) and support (Felsenstein, 1985;Sanderson, 1995;Bremer et al., 1999) (Figs. 1a, 1b). Although the number of characters needed for accurate phylogeny reconstruction is difficult to estimate, the number of characters needed in simulation studies to recover accurate trees is an order of magnitude greater than that available from morphology

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“…Tellingly, this selective acceptance effectively translates to a rejection of any phylogenetic study of avian origins, which must rely on fossil data and hence on morphological characters. An extensive body of literature supports the efficacy of morphology in phylogenetic analysis (e.g., Huelsenbeck 1991, Smith 1998, Wiens 2000, Jenner 2004, Smith and Turner 2005 and those data will continue to be integral to testing evolutionary hypotheses.…”

Section: Theoretical and Methodological Misunderstandingsmentioning

confidence: 99%

Rhetoric vs. reality: A commentary on “Bird Origins Anew” by A. Feduccia

Smith

Chiappe

Clarke

et al. 2015

The Auk

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Birds are maniraptoran theropod dinosaurs. The evidence supporting the systematic position of Avialae as a derived clade within Dinosauria is voluminous and derived from multiple independent lines of evidence. In contrast, a paucity of selectively chosen data weakly support, at best, alternative proposals regarding the origin of birds and feathers. Opponents of the theory that birds are dinosaurs have frequently based their criticisms on unorthodox interpretations of paleontological data and misrepresentation of phylogenetic systematic methods. Moreover, arguments against the nested position of Avialae in Dinosauria have often conflated the logically distinct questions of avian origins, the evolution of flight, and the phylogenetic distribution of feathers. Motivated by a Perspectives article with numerous factual inaccuracies that recently appeared in The Auk, we provide a review of the full complement of facts pertaining to the avian origins debate and address the misplaced criticisms raised in that opinion paper. Keywords: evolution of flight, evolution of feathers, evolution of birds, Avialae, maniraptoran theropod dinosaurs, phylogenetic systematics Retórica vs. Realidad: Un comentario sobre ''Bird Origins Anew'' por A. Feduccia, Auk 130:1-12 RESUMEN Las aves son dinosaurios terópodos maniraptores. La evidencia que sustenta la posición sistemática de Avialae como un clado derivado dentro de Dinosauria es voluminosa y se deriva de múltiples líneas independientes de evidencia. En contraste, sólo escasos datos elegidos selectivamente sustentan débilmente propuestas alternativas sobre el origen de las aves y las plumas. Los opositores de la teoría de que las aves son dinosaurios frecuentemente han basado sus críticas en interpretaciones no ortodoxas de los datos paleontológicos y en la tergiversación de los métodos de la sistemática filogenética. Además, los argumentos en contra de la posición anidada de Avialae dentro de Dinosauria han confundido la distinción lógica de las preguntas sobre los orígenes de las aves, la evolución del vuelo y la distribución filogenética de las plumas. Motivados por un artículo de Perspectivas que apareció recientemente en The Auk con numerosas imprecisiones fácticas, presentamos una revisión del conjunto completo de hechos relacionados con el debate sobre el origen de la aves y abordamos las críticas equivocadas que se presentan en dicho artículo de opinión. Palabras clave: Avialae, dinosaurios terópodos maniraptores, evolución de las aves, evolución de las plumas, evolución del vuelo, sistemática filogenética Q 2015 American Ornithologists' Union.

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What Does Palaeontology Contribute to Systematics in a Molecular World?

Cited by 54 publications

References 49 publications

Diversification of Ramphastinae (Aves, Ramphastidae) prior to the Cretaceous/Tertiary boundary as shown by molecular clock of mtDNA sequences

Diversification of Ramphastinae (Aves, Ramphastidae) prior to the Cretaceous/Tertiary boundary as shown by molecular clock of mtDNA sequences

Phylogeny Reconstruction: The Role of Morphology

Rhetoric vs. reality: A commentary on “Bird Origins Anew” by A. Feduccia

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