The Effect of Combining Molecular and Morphological Data in Published Phylogenetic Analyses

Abstract

Understanding the natural world is not possible with out an extensive knowledge of organismal morphology. The encyclopedia of life (Wilson, 2003) would be an empty, sterile list without detailed information about the full range of morphological diversity. Morphology plays a pivotal role in our understanding of life cycles, geographical distributions, identification, conservation status, evolution, development, and species delimitation (Buzgo et al, 2004; Endress, 2000; Kaplan, 2001; Scotland et al., 2003a). Nonetheless, there remains considerable debate about the precise role of morphology in one par ticular area of biology ? computer-based phylogenetic inference (Baker and Gatesy, 2002; Hillis and Wiens, 2000; Jenner, 2004; Scotland et al, 2003b; Smith and Turner, 2005; Wortley and Scotland, 2006; Wiens, 2004). One widespread contemporary use of morphological data in phylogeny reconstruction is in combined anal ysis with sequence data (recent examples in clude Aagesen and Sanso, 2003; Cameron and Williams, 2003; Cohen et al, 2004; Dorchin et al, 2004; Hebsgaard et al., 2004; Lundberg and Bremer, 2003; Michelangeli et al, 2003; Near et al, 2003; Pedersen et al., 2003; Zrzavy, 2003). Despite the methodological, conceptual, and philosophical issues surrounding combined analy ses of independent data partitions (Ballard, 1996; Bal lard et al., 1998; Brower et al., 1996; Bull et al, 1993; De Queiroz et al., 1995; Farris, 2000; Huelsenbeck et al., 1996; Kluge, 1998; Levasseur and Lapointe, 2001; Nixon and Carpenter, 1996; Page, 1996; Pupko et al, 2002), the number of combined analyses conducted recently demonstrates that this is a popular way of integrating morphological data into phylogenetic analyses. Recent empirical studies have both questioned (e.g., Gaubert et al., 2005) and defended (e.g., Wahlberg et al., 2005) the role of morphology in phylogenetic analysis, with equal vigor. Although individual studies such as these can be highly informative and compelling, it is doubtful whether they can effectively reflect general trends. In 1998, Baker et al. investigated the contribution of morphological data sets to combined analyses with data across a range of studies and found that the support contributed by morphological data was substantial, and often greater than that provided by data. Since then, sequence data sets have dramatically increased in size (from an average of 156 parsimony-informative characters across the 15 data sets studied in Baker et al. (1998) to an average of 391 parsimony-informative characters across the 26 data sets analyzed in this paper), whereas morpho logical data sets have remained approximately the same (from an average of 40 parsimony-informative charac ters in Baker et al., 1998, to 47 parsimony-informative characters here). Since the first phylogenetic analyses using data, more than 20 years ago (e.g., Curtis and Clegg, 1984; Hillis, 1987; Rogers and Bendick, 1985), the composition of data sets has also changed. Molecular data sets can include amplified fragment length polymorphisms (AFLPs), restriction fragment length polymorphisms (RFLPs), protein and DNA sequences, coded gaps, and secondary chemicals. At the time of Baker et al.'s (1998) study, only two-thirds of molecular analyses considered comprised DNA sequence data. Today, the vast majority of analyses of data comprise DNA sequences (all of the data sets studied in this paper included DNA sequence, 24 out of 26 exclusively). Changes in the size and composition of data sets used in phyloge netic analysis imply that the relative contribution of mor phological data to combined analyses with data may also have changed significantly in recent years. In the context of the ongoing debate surrounding and morphological data in phylogenetic stud ies, there is a need for a broad survey to assess this de velopment, and in particular to determine the effect of adding morphological data to sequence data in combined analysis today. This has the potential to provide important general insights about current prac tice that individual, taxon-specific analyses do not. Two