DNA and morphology: Inference of plant phylogeny

Sytsma, Kenneth J.

doi:10.1016/0169-5347(90)90163-8

Cited by 107 publications

(68 citation statements)

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“…We suspect that the optimism of congruence between morphology and molecules in plants is well placed simply because many taxa long recognized on the basis of morphology have been supported using molecular data and that this is widely appreciated (Hillis, 1987;Sanderson and Donoghue 1989;Sytsma, 1990;Donoghue and Sanderson, 1992;Patterson et al, 1993;Hillis and Wiens, 2000). Less clear is the extent to which phylogenetic analyses of morphological data have increased our understanding of phylogeny.…”

Section: The Role Of Morphology In Systematicsmentioning

confidence: 99%

“…Although the extent of congruence between morphological and molecular phylogenetic analyses has not been quantified, some researchers anticipated a high level of congruence between molecules and morphology (e.g., Hillis, 1987;Sanderson and Donoghue, 1989;Sytsma, 1990;Donoghue and Sanderson, 1992;Hillis and Wiens, 2000), whereas others were less optimistic or sceptical (e.g., Patterson et al, 1993;Lamboy, 1994;Hedges and Maxon,1996;Sytsma, 1997a, 1997b;Baker et al, 1998). We suspect that the optimism of congruence between morphology and molecules in plants is well placed simply because many taxa long recognized on the basis of morphology have been supported using molecular data and that this is widely appreciated (Hillis, 1987;Sanderson and Donoghue 1989;Sytsma, 1990;Donoghue and Sanderson, 1992;Patterson et al, 1993;Hillis and Wiens, 2000).…”

Section: The Role Of Morphology In Systematicsmentioning

confidence: 99%

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Phylogeny Reconstruction: The Role of Morphology

Scotland¹,

Olmstead²,

Bennett³

2003

Systematic Biology

264

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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Section: The Role Of Morphology In Systematicsmentioning

confidence: 99%

Section: The Role Of Morphology In Systematicsmentioning

confidence: 99%

Phylogeny Reconstruction: The Role of Morphology

Scotland¹,

Olmstead²,

Bennett³

2003

Systematic Biology

264

269

View full text Add to dashboard Cite

show abstract

“…The fact that intraindividual heterogeneity for ITS repeat copies can remain for a given period of time following a hybridization event despite the action of concerted evolution (Zimmer & al., 1980) also makes this marker useful in detecting cases of reticulate evolution among divergent lineages (Sang & al., 1995;Whittall & al., 2000;Fuertes Aguilar & Nieto Feliner, 2003). Even if concerted evolution has been active and different copies are homogenised, ITS sequence data may still provide valuable information on reticulate evolution when showing incongruent patterns with respect to other differently inherited markers (e.g., cpDNA, Rieseberg, 1991) or morphological and biogeographical evidence (Sytsma, 1990;Fuertes Aguilar & al., 1999b;Nieto Feliner & al., 2004). The genus Phlomis L. (Lamiaceae) comprises over Systematic and evolutionary relationships within the diploid Western Mediterranean Phlomis crinita/lychnitis complex remain controversial apparently due to hybridization and introgression.…”

Section: Introductionmentioning

confidence: 99%

Contrasting nuclear‐plastidial phylogenetic patterns in the recently diverged IberianPhlomis crinitaandP. lychnitislineages (Lamiaceae)

Albaladejo

Aguilar

Aparicio

et al. 2005

TAXON

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Systematic and evolutionary relationships within the diploid Western Mediterranean Phlomis crinita/lychnitis complex remain controversial apparently due to hybridization and introgression. This study examines patterns of sequence variation in the nuclear ribosomal DNA (ITS region) and three non‐coding plastid DNA regions (trnH‐psbA, trnT‐trnL and atpB‐rbcL) in this complex in an aim to clarify whether hybridization, introgression or lineage sorting resulting from recent diversification is mainly responsible for poorly understood relationships. Information recovered from nuclear and chloroplast markers was found to be strongly incongruent. Phylogenetic analysis of inferred nuclear ITS ribotypes is consistent with previous morphometric and taxonomic results in distinguishing two sister lineages, P. crinita s.l. and P. lychnitis. In addition, the high number of additive polymorphisms detected in ITS sequences suggests the sharing of ancestral variability and local patterns of gene flow within the complex. In contrast, the pattern of chloroplast haplotype variation is geographic rather than taxonomic, which might be caused by low mutation rates combined with frequent instances of interspecific hybridization. To integrate the apparently discordant plastid and nuclear evidence, we suggest that both lineage sorting and horizontal transfer have been involved. Even though pinpointing cases due to either phenomenon is difficult, the available data provide evidence of two sister lineages where hybridization events can be identified despite the inheritance of ancestral polymorphisms.

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“…Within this general phylogenetic frame of reference, a widespread belief has arisen that analyzing the evolution of particular characters in the context of phylogenetic trees based wholly or partly on those same characters is logically circular, and that independent phylogenies (i.e., ones based on data other than the characters under investigation) are needed to analyze character evolution properly (e.g., Coddington 1988;Carpenter 1989;Lander and Liem 1989;Olmstead 1989;Sytsma 1990;Brooks and McLennan 1991;McKey 1991;Vane-Wright et al 1992).…”

Section: Notes and Comments Including The Characters Of Interest Durimentioning

confidence: 99%

Including the Characters of Interest During Tree Reconstruction and the Problems of Circularity and Bias in Studies of Character Evolution

Queiroz¹

1996

The American Naturalist

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DNA and morphology: Inference of plant phylogeny

Cited by 107 publications

References 1 publication

Phylogeny Reconstruction: The Role of Morphology

Phylogeny Reconstruction: The Role of Morphology

Contrasting nuclear‐plastidial phylogenetic patterns in the recently diverged IberianPhlomis crinitaandP. lychnitislineages (Lamiaceae)

Including the Characters of Interest During Tree Reconstruction and the Problems of Circularity and Bias in Studies of Character Evolution

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