Evolution of Flowers and Inflorescences |
Morphological and molecular phylogenetic context of the angiosperms: contrasting the ‘top-down’ and ‘bottom-up’ approaches used to infer the likely characteristics of the first flowers
1Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey TW9 3AB, UK
2School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
* To whom correspondence should be addressed. E-mail: r.bateman{at}rbgkew.org.uk
Received 4 May 2006; Accepted 13 July 2006
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Abstract |
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 Top Abstract IntroductionWhat is a flower?Which are the (other)...Which are the benchmark...Which kinds of phylogeny...How significant are optimization...What is the best...What is the best...Do some nodes in...Why is it important...What are the effects...What are the pros...Which key characters best...Why are palaeobotanists obsessed...Are clades such as...Do some categories of...What is the preferred...References |
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Recent attempts to address the long-debated ‘origin’ of the angiosperms depend on a phylogenetic framework derived from a matrix of taxa versus characters; most assume that empirical rigour is proportional to the size of the matrix. Sequence-based genotypic approaches increase the number of characters (nucleotides and indels) in the matrix but are confined to the highly restricted spectrum of extant species, whereas morphology-based approaches increase the number of phylogenetically informative taxa (including fossils) at the expense of accessing only a restricted spectrum of phenotypic characters. The two approaches are currently delivering strongly contrasting hypotheses of relationship. Most molecular studies indicate that all extant gymnosperms form a natural group, suggesting surprisingly early divergence of the lineage that led to angiosperms, whereas morphology-only phylogenies indicate that a succession of (mostly extinct) gymnosperms preceded a later angiosperm origin. Causes of this conflict include: (i) the vast phenotypic and genotypic lacuna, largely reflecting pre-Cenozoic extinctions, that separates early-divergent living angiosperms from their closest relatives among the living gymnosperms; (ii) profound uncertainty regarding which (a) extant and (b) extinct angiosperms are most closely related to gymnosperms; and (iii) profound uncertainty regarding which (a) extant and (b) extinct gymnosperms are most closely related to angiosperms, and thus best serve as ‘outgroups’ dictating the perceived evolutionary polarity of character transitions among the early-divergent angiosperms. These factors still permit a remarkable range of contrasting, yet credible, hypotheses regarding the order of acquisition of the many phenotypic characters, reproductive and vegetative, that distinguish ‘classic’ angiospermy from ‘classic’ gymnospermy. The flower remains ill-defined and its mode (or modes) of origin remains hotly disputed; some definitions and hypotheses of evolutionary relationships preclude a role for the flower in delimiting the angiosperms. We advocate maintenance of parallel, reciprocally illuminating programmes of morphological and molecular phylogeny reconstruction, respectively supported by homology testing through additional taxa (especially fossils) and evolutionary-developmental genetic studies that explore genes potentially responsible for major phenotypic transitions.
Key words: Angiosperm, character optimization, congruence, development, evolutionary-developmental genetics, flower, fossil, gene duplication, gymnosperm, morphology, ontogeny, outgroup, phylogeny, pteridophyte, taxon sampling, tree rooting
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Introduction |
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TopAbstractIntroductionWhat is a flower?Which are the (other)...Which are the benchmark...Which kinds of phylogeny...How significant are optimization...What is the best...What is the best...Do some nodes in...Why is it important...What are the effects...What are the pros...Which key characters best...Why are palaeobotanists obsessed...Are clades such as...Do some categories of...What is the preferred...References |
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‘An early hope was that the relationships indicated among species by DNA were more likely to be correct than those based on morphology; this now seems naïve.’ (Judd et al., 1999, p. 99)‘The primary motivating force for preparing this book was the dramatic change in our understanding of angiosperm phylogeny during the past 10 years. Many long-standing [morphological] views of deep-level relationships were altered suddenly and substantively as a direct result of molecular analyses.’ (Soltis et al., 2005, p. ix)
‘Occam's razor? But that's for circumcision, surely?’ (Tom Sharpe, 1995; Grantchester Grind, London: Macmillan, p. 82)
In this review we address one of the most popular discussion topics in evolutionary biology: the origin of the flower, and, by implication, the origin of the flowering plants (note that we pay much less attention to the better documented subsequent, family-level radiation of the angiosperms; cf. Friis et al., 2006). We do not attempt to offer definitive answers on the fundamental nature of the flower but, instead, aim to establish a more rigorous context for future research. Our main objective is to review and, where possible, clarify several of the key issues in this broad field.
We willingly follow the modern convention of placing our discussion in the context of an explicit phylogenetic framework, but within this framework we have chosen to exercise certain prejudices. Unlike most recent contributions to this debate, we do not focus on a single phylogenetic hypothesis, preferring instead to consider the implications of a variety of matrix-based phylogenies derived from highly contrasting kinds of data. In assessing the relative merits of these hypotheses, we emphasize conceptual rigour over statistical robustness. We are especially concerned with identifying the optimal roles for different categories of data that pertain either directly or indirectly to phylogeny reconstruction. We therefore discuss both molecular and morphological data sources, including fossils, are discussed. This issue is explored in the context of two contrasting perspectives on land-plant phylogeny: the top-down perspective looks backward through evolutionary time from the present, whereas the bottom-up perspective looks forward through evolutionary time from the deep past.
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What is a flower? |
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TopAbstractIntroductionWhat is a flower?Which are the (other)...Which are the benchmark...Which kinds of phylogeny...How significant are optimization...What is the best...What is the best...Do some nodes in...Why is it important...What are the effects...What are the pros...Which key characters best...Why are palaeobotanists obsessed...Are clades such as...Do some categories of...What is the preferred...References |
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Given the vast tracts of published text devoted to the origin of the flower (and of the flowering plants), this is one question that could reasonably be assumed to have been unequivocally answered. Indeed, most glossaries included in textbooks and reviews omit the term ‘flower’, presumably on the assumption that the term is universally understood and the underlying concept is familiar to even the most lackadaisical student of botany. However, comparison of the definitions assembled in Table 1 reveals little unanimity. Four ostensibly distinct elements can be extracted from this aggregate of definitions: form, function, homology, and taxonomy.
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The majority of definitions identify (sexual) reproduction as the primary function of the flower; an uncontentious statement, but one that does not in itself separate a flower from the reproductive structure(s) of any other land plant.
Two definitions include explicit references to taxonomically (and phylogenetically) delimited groups of organisms: the clade of groups that bear flower-like structures (Anthophytes) and, more controversially, the more inclusive clade of groups that bear seeds (Spermatophytes). The definition from Chambers Dictionary encompasses gymnosperms as well as angiosperms. It therefore begs immediate rejection by all knowledgeable botanists, who routinely equate the structure ‘flower’ with the (monophyletic) group ‘angiosperms’, and who consequently attempt to define gymnosperms in part by their absence of flowers.
With regard to form, several definitions describe the flower as a composite structure, referring explicitly to the presence of four differentiable categories of (usually physically discrete) organs that are organized in a specific and reliable linear sequence along the axis towards its apex: sepals, petals, stamens, and carpels. A few definitions emphasized the function of stamens and carpels for generating gametes (male and female, respectively), and Foster and Gifford (1971) and Frohlich (2006) further identified the carpel as being the most diagnostic feature of a flower. Foster and Gifford also noted that definitions of a flower omitting reference to these structures, such as that of Goebel (1905), implicitly encompass not only all angiosperms but also all gymnosperms and even some of the more derived, reproductively complex, pteridophyte groups (thereby rendering less bizarre the aforementioned Chambers Dictionary definition: Table 1).
Crucial to the majority of definitions is an almost universally accepted interpretation of the flower as a determinate reproductive shoot with a defined number of floral organs, typically (but not universally) arranged in at least four distinct whorls: sepals, petals, stamens, and carpels. Specifically, the flower is homologized with an axis bearing sporophylls (i.e. evolutionarily modified sporangium-bearing leaves or, perhaps more conservatively, leaf-like structures). Implicit in these definitions is the dynamic concept of a transition from an earlier, profoundly different (and thus recognizable) ancestral form of reproductive organ. The identity of the ancestral group is almost universally accepted, namely the gymnosperms; an origin among the (by definition) seed-less pteridophytes requires a set of morphological transitions that seemingly is too radical for any modern botanist to seriously contemplate.
Thus, we can draw on several categories of information in order to define a flower. And, having defined a flower, surely we have by default defined a flowering plant—an angiosperm. Why then have the more informed among the land-plant morphologists appended firm cautionary notes to their preferred definitions? For example, according to Foster and Gifford (1971, p. 593), ‘As angiosperms are commonly designated the flowering plants, it might be assumed that there is rather general agreement about the scientific concept of a flower. Unfortunately, this is not the case, and the literature on floral organography, ontogeny, and structure displays widely divergent viewpoints of the fundamental nature of the flower as well as on the interpretation of its component organs (sepals, petals, stamens, and carpels). One of the basic difficulties lies in our complete [sic] ignorance of the evolutionary history of the flower ...; it becomes largely a matter of conjecture whether it is justifiable to draw comparisons between modern angiospermous flowers and the spore-producing structures of other tracheophytes [vascular land-plants]. If such comparisons are attempted, it is quite possible to reach either a very broad or a very restricted concept or definition of a flower.’
Bierhorst (1971, p. 511) preceded his definition by stating that a flower is ‘a structure that, because of its various degrees of completeness, cannot adequately be defined in words’. This, and many other similar statements in the literature, refer primarily to the considerable floral variation revealed by surveys of extant angiosperms. Some species lack sepals, petals, or both. For example, in one clade (Saururaceae plus Piperaceae) of the magnoliid order Piperales, flowers are entirely perianth-less, a feature that is closely correlated (at least, in this group) with possession of indeterminate inflorescences (Remizowa et al., 2005). Many other species show morphological gradation between sepals, petals, and/or stamens. Yet others contravene the requirement for bisexuality by bearing functional stamens and carpels on separate flowers, either on the same individual (monoecy) or on separate individuals (dioecy); organs of the opposite gender have either been rendered sterile or completely suppressed. For example, the much-discussed ‘primitive’ extant angiosperm Amborella (Fig. 1A, B) is commonly (though not reliably) dioecious, bearing either exclusively male flowers (lacking even sterile carpels) or female flowers that occasionally bear staminodes, sometimes with a developmental transition between stamens and carpels (Buzgo et al., 2004). Many other early-divergent extant angiosperms even lack carpel closure by tissue fusion (Endress and Igersheim, 2000a, b; Endress, 2001a) or double fertilization (Williams and Friedman, 2002). The columellar infratectum in the microspore wall of angiosperms, functionally linked to chemical recognition systems on the stigmatic surface, is also unreliably present in basally divergent extant angiosperms (Sampson, 2000; Doyle, 2006; Frohlich, 2006).
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Thus, several supposedly definitive features of the flower are frequently absent from angiosperms, especially early-divergent angiosperms: these include hermaphroditism, fully closed carpels, and a distinctly whorled arrangement. Admittedly, the presence on the ovule of a second (outer) integument, and the remarkably conservative structure of the stamen (two thecae joined by a connective, each consisting of two embedded microsporangia), are more consistent features of the angiosperm flower, though they too have potential homologues in some gymnosperm groups (Doyle, 2006).
Furthermore, the flower-subtending bract, normally regarded as extra-floral, can strongly influence, or even be considered part of, the flower (e.g. Remizowa et al., 2005; Buzgo et al., 2006). Bringing a palaeobotanical perspective to bear, Stewart and Rothwell (1993, p. 440) coined the phrase ‘accessory reproductive structures’ to encompass sterile organs associated with reproductive functions—not only perianth members (tepals, or petals plus sepals) but also another (less well-researched) leaf-like organ, the flower-subtending bract. Bracts (and bracteoles) share with perianth members the characteristics of exhibiting many leaf-like features but being positionally fixed with respect to either a flower or an inflorescence. In some angiosperms, the bract has become intimately integrated into the flower; for example, Amborella (Fig. 1A, B) and several other early-divergent angiosperms (e.g. Austrobaileya, Trimenia) exhibit a morphological continuum between bracts and perianth (Endress, 2001b; Buzgo et al., 2004). In others (e.g. Araceae, Cornaceae, Saururaceae) the inflorescence bracts are conspicuously petaloid and hence perform at least one of the functions (pollinator attraction) that are more typically performed by petals. For example, in two genera (Houttuynia and Anemopsis) of the perianth-less family Saururaceae, the inflorescence bracts form a pseudocorolla, and the entire inflorescence has a flower-like appearance (Tucker, 1981).
More significantly, many of the gymnospermous groups, both extant and extinct, which are by definition considered to lack a differentiated perianth, unequivocally possess bract-like organs. Arber and Parkin (1907) coined the terms ‘anthostrobilus’ for the modern angiosperm flower, and ‘pro-anthostrobilus’ for the type of cone manifested not only by the Mesozoic bennettite Williamsoniella (Fig. 1D) but also by a hypothetical group of extinct stem-group angiosperms that they termed ‘Hemiangiospermae’. They noted that the bennettite cone possessed a series of sterile leaf-like organs that they interpreted as an ‘undifferentiated primitive perianth’. They also insightfully defined a major subset of (derived) angiosperms as possessing ‘a euanthostrobilus, of which the distinctive features are the presence of the special type of microsporophyll termed a stamen, and of closed carpels’ (Arber and Parkin, 1907, p. 75). Thus, if flowers are at least partly defined not by possession of sepals and/or petals but by possession of the broader category of leaf-like accessory reproductive structures, the flower is no longer seen as a unique (and defining) attribute of the angiosperms, and when using the term ‘flowering plants’ certain gymnospermous groups, especially extinct taxa such as Bennettitales, should strictly be included (cf. Crane, 1988). This conclusion is implicit in our own (inevitably imperfect) definition of a flower: a determinate axis bearing megasporangia that are surrounded by microsporangia and are collectively subtended by at least one sterile laminar organ. In formulating this definition, the orientation of our discussion has, in practice, switched from top-down to bottom-up. We note that, although we do not necessarily exclude multiple origins of flower-like structures (see below), our definition has converged on that of Arber and Parkin (1907, p. 75), who characterized the anthostrobilus as ‘a special form of amphisporangiate cone, distinguished by the peculiar juxtaposition of the mega- and microsporophylls, and by possessing a well-marked perianth’. We also note that Arber and Parkin primarily (and almost uniquely) employed a bottom-up approach in what became a benchmark study in floral evolution that remained influential throughout the ensuing century.
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Which are the (other) benchmark studies in floral evolution? |
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TopAbstractIntroductionWhat is a flower?Which are the (other)...Which are the benchmark...Which kinds of phylogeny...How significant are optimization...What is the best...What is the best...Do some nodes in...Why is it important...What are the effects...What are the pros...Which key characters best...Why are palaeobotanists obsessed...Are clades such as...Do some categories of...What is the preferred...References |
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Certain conceptual thresholds can readily be identified in the study of flowers and flowering plants. In his benchmark classification of flowering plants, Linnaeus (Linné, 1735) emphasized the significance of the number and arrangement of stamens and carpels. The possible equivalence of sepals, petals, and stamen filaments (though not explicitly the carpels) to modified leaves was greatly elaborated by Goethe (1790) in an essentialist essay partly stimulated by studying plant teratologies. However, Goethe's ideas about simple equivalence, summarized by the famous phrase ‘all is leaf’, had no phylogenetic implications (Lönnig, 1994). As noted by adherents of Zimmerman's telome theory (Zimmerman, 1930, 1938), such as Wilson (1937), spore-bearing organs (i.e. sporangia) evolved before leaves in early land plants. By contrast, Darwin's (1859) development of a credible evolutionary mechanism to explain (albeit in a uniformly gradualistic manner) such radical morphological transitions was followed by the harnessing of Mendelian genetics to address the control of such transitions by authors such as De Vries (1906) and later Wardlaw (1965).
These new data sources informed some increasingly sharp exchanges between proponents of the two main sets of theories competing to explain the origin of the flower. The more common euanthial theory that was pioneered by Goethe (and is implicit in most of the definitions of a flower collated in Table 1) postulates derivation from an unbranched, uniaxial structure, and hence interprets the flower as a condensed sporophyll-bearing single axis with proximal microsporophylls (stamens) and distal megasporophylls (carpels) (Arber and Parkin, 1907; Arber, 1937). By contrast, the more diverse pseudanthial theories all perceive the flower as having condensed from a multiaxial structure (Wettstein, 1907; Melville, 1960; Eames, 1961; Meeuse, 1975, 1987, Stuessy, 2004). Thus, the difference between the two conflicting hypotheses relates more to the nature of individual organs than to the flower as a whole. Several authors have postulated secondary derivation of flower-like structures from inflorescences (i.e. a secondary pseudanthial origin in certain phylogenetic groups), based on ontogenetic evidence. These studies relate to both gymnosperms (Gnetales: Mundry and Stützel, 2004) and angiosperms (e.g. alismatid monocots: many authors, reviewed by Sokoloff et al., 2006). Multiple origins of flower-like structures, both within angiosperms and other seed plants, are implicit in these pseudanthial hypotheses.
Studies of flowers prompted by the various insights outlined above were, to varying degrees, comparative, and in some cases hypothesis-testing. However, they often (i) focused on limited suites of morphological characters considered a priori to be of particular importance, (ii) failed to determine whether the characters of interest were ever specified by a single genome (i.e. were observed in a single individual), and/or (iii) unjustifiably equated extreme diversity of form with increased likelihood of multiple origins of the feature in question. More importantly, they lacked a unifying conceptual framework. This crucial prerequisite has been provided, first by phylogeny reconstruction and then by evolutionary-developmental genetics, epitomized by the ABC model of floral whorl control (e.g. Coen and Meyerowitz, 1991; Irish and Kramer, 1998; Kramer and Irish, 1999; Lawton-Rauh et al., 2000; Cronk et al., 2002; Theissen et al., 2002).
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Which are the benchmark studies in reconstructing seed-plant phylogeny? |
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TopAbstractIntroductionWhat is a flower?Which are the (other)...Which are the benchmark...Which kinds of phylogeny...How significant are optimization...What is the best...What is the best...Do some nodes in...Why is it important...What are the effects...What are the pros...Which key characters best...Why are palaeobotanists obsessed...Are clades such as...Do some categories of...What is the preferred...References |
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The now ubiquitous tree motif routinely used to represent the supposed sequence of divergence of evolutionary lineages was famously employed by Darwin (1859) and elaborated by authors such as Haeckel (1894). However, only with the early cladistic works of entomologists Hennig (1966) and Brundin (1972) were we provided with the rigorous conceptual framework needed to generate such trees with a large degree of objectivity from matrices of coded taxa, each explicitly scored for competing states of a broad suite of characters. Central to this approach is the concept of the congruence test of homology (e.g. Patterson, 1988). The preferred phylogeny for the scored taxa is the one requiring fewest transitions between character-states. We can then observe in the resulting tree(s) which character-states delimit which taxonomic groups—in other words, which prior statements of homology between species have been upheld in the most-parsimonious tree(s). The particulate nature of the numerically scored character states is preserved in the resulting trees, thereby simplifying various kinds of post hoc character analysis.
The cladistic approach was first used to compare the major groups of seed-plants by Hill and Crane (1982). With the assistance of rapidly improving computer hardware and software, it spawned an increasing number of morphological phylogenies based on parsimony analyses during the 1980s and early 1990s. If we consider the development of taxonomically broad morphological matrices for seed-plants, four main lineages can be recognized, nucleating around PR Crane (e.g. Hill and Crane, 1982; Crane, 1985, 1988), JA Doyle (e.g. Doyle and Donoghue, 1986, 1987, 1992; Doyle, 1996, 1998a, b, 2006; Hilton and Bateman, 2006), GW Rothwell (e.g. Rothwell and Serbet, 1994; Rothwell and Nixon, 2006), and DW Stevenson (e.g. Loconte and Stevenson, 1990, 1991; Nixon et al., 1994). These studies placed as closest relatives of angiosperms, in various paraphyletic combinations, several groups (most of them wholly extinct) that possess reproductive organs showing some flower-like properties, notably Gnetales, Bennettitales (Fig. 1D), Pentoxylon, Caytonia (Fig. 1C), and glossopterids. Such arrangements soon became known collectively as the anthophyte hypothesis, implying that the flower evolved only once and, hence, that all flowers are fundamentally homologous.
By 1990, these morphological analyses were competing with (and soon largely superseded by) phylogenetic studies employing as characters the sequences of nucleotides (and insertion–deletion mutations) in specific regions of the three plant genomes: nuclear-chromosomal, plastid, and mitochondrial. As the number of readily sequenced regions (and hence the number of usable characters) increased exponentially, driven by advances in sequencing technology, maximum parsimony was supplemented with more mathematically complex methods of generating trees, notably maximum likelihood and, latterly, Bayesian approaches (e.g. Page and Holmes, 1998). The current species richness and ecological pre-eminence of angiosperms have caused them to be preferentially sampled for phylogenetic studies. The result is a framework of relationships that is generally viewed as well-sampled and increasingly (though by no means universally) as reliable (e.g. Soltis et al., 2004, 2005), and underpins higher classifications that are based on ‘natural’ monophyletic groups (e.g. APGII: Angiosperm Phylogeny Group, 2003).
At present, increasing numbers of species have been sequenced for the complete plastid and/or mitochondrial genomes (e.g. Goremykin et al., 2005), and a few for the entire nuclear genome (e.g. rice, Arabidopsis; Arabidopsis Genome Initiative, 2000; Bennetzen 2002; Yu et al., 2002; Yamada et al., 2003; International Rice Genome Sequencing Project, 2005). These sequence-based data not only allow character-rich (if presently species-poor) phylogeny reconstructions of extant species but also provide a yardstick for comparative studies that focus simultaneously on changes in key developmental genes and the phenotypic characters that they ‘control’—a growing discipline termed evolutionary-developmental genetics (e.g. Cronk et al., 2002). This approach is especially attractive, as it represents an alternative, and potentially more informative, test of a priori homology statements that also explicitly links genotype with the resulting phenotype, and thence ultimately with specific biological function(s). Thus, the major phenotypic transitions first explored morphologically by Goethe (1790), functionally by Darwin (e.g. 1859), and genetically by De Vries (1906) can at last begin to be examined for fundamental causation (e.g. Frohlich and Parker, 2000; Bateman and DiMichele, 2002; Vergara-Silva, 2003; Baum and Hileman, 2006; Hintz et al., 2006; Theissen, 2006).
Despite their conflicting topologies (Fig. 2), these different approaches share some common elements with respect to seed-plant relationships. Angiosperm monophyly is routinely inferred. Nonetheless, a few brave authors generally viewed as mavericks, notably Meeuse (1976, 1987), have penned morphologically based (though not matrix-based) arguments for polyphyly. Cladistic analyses, both morphological and molecular, consistently place the clade containing all extant angiosperm lineages (the ‘crown-group’ angiosperms: Fig. 3) on a long branch with respect to the remaining seed plants. ‘Missing links’ (i.e. stem-group) angiosperms have been postulated from the fossil record but have not hitherto obtained universal acceptance (e.g. Archaefructus, discussed below). Furthermore, relationships among extant gymnosperms, and hence homologies among their reproductive structures, remain contentious. These issues can only be partly circumvented by adopting a top-down approach but are fundamental to any bottom-up approach.
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Which kinds of phylogeny are of greatest value? |
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TopAbstractIntroductionWhat is a flower?Which are the (other)...Which are the benchmark...Which kinds of phylogeny...How significant are optimization...What is the best...What is the best...Do some nodes in...Why is it important...What are the effects...What are the pros...Which key characters best...Why are palaeobotanists obsessed...Are clades such as...Do some categories of...What is the preferred...References |
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Why do tensions remain within the phylogenetic community regarding molecular versus morphological characters and extant versus extinct taxa? Over the past two decades, molecular phylogenies have in practice largely superseded morphological phylogenies. This shift of emphasis has had profound consequences, yet it is now rarely discussed. Arguments most commonly advanced against morphological rather than molecular phylogenetic analyses are:
- (i) the limited number of characters available (and the existence of an asymptote of the number of phylogenetically informative character states available as taxa are successively added to a matrix: Bateman, 1992);
- (ii) the high cost in time expended per unit character coded (both in terms of actual character scoring and the ‘informal apprenticeship’ that must first be undertaken in order to describe and code characters correctly);
- (iii) an inevitable degree of subjectivity involved in making a priori homology assessments (in other words, in delimiting characters before each is in turn divided into alternative character states);
- (iv) the supposed comparatively high level of homoplasy (this is caused by conflicting character states, which are considered to mainly reflect similar responses to similar pressures of directional or disruptive selection in lineages that are in fact only distantly related: Scotland et al., 2003), and;
- (v) the potential developmental correlation of apparently unrelated characters (e.g. pleiotropic expression of a single critical mutation).
- (ii) the high cost in time expended per unit character coded (both in terms of actual character scoring and the ‘informal apprenticeship’ that must first be undertaken in order to describe and code characters correctly);
At least some observers perceive corresponding constraints on molecular phylogenies:
- (i) the limited number, and sporadic phylogenetic distribution, of taxa available, due to the inability to allow molecularly recalcitrant extinct taxa to participate in the tree-building procedure (a central issue of this paper);
- (ii) the fact that routinely sequenced regions of the three genomes do not participate directly in the phenotypic transitions that signal a macroevolutionary event (Bateman, 1999);
- (iii) an inevitable degree of subjectivity in aligning nucleotides in matrices that are rich in insertion–deletion events (in other words, in assigning some states of some taxa to the correct character);
- (iv) the availability of the same restricted set of a maximum of four (or arguably five: A, C, G, T, and absent) states for each position/character artificially masks much of the actual homoplasy (e.g. when a particular A mutates to a T but later reverts to an A);
- (v) the potential in expressed regions of the genome for particular categories of nucleotide to behave differently (e.g. contrasting mutational rates in different compartments and regions of the genome, first and second versus third bases within codons, and radical contrasts in the GC:AT ratio).
- (ii) the fact that routinely sequenced regions of the three genomes do not participate directly in the phenotypic transitions that signal a macroevolutionary event (Bateman, 1999);
Additional phenomena that can negatively affect both morphological and molecular matrices include:
- (i) strong heterogeneity of rates of change within the study group, encouraging the most rapidly changing branches to falsely coalesce; this now thoroughly researched, but still problematic, phenomenon is termed long-branch attraction (e.g. Sanderson et al., 2000; Felsenstein, 2004);
- (ii) migration of genes (and the phenotypic characters that they underpin) between lineages through hybridization, lateral gene transfer, and organelle capture, and;
- (iii) the necessity of rooting the tree, typically through outgroup choice, in order to polarize characters and thereby study character evolution (another central issue of this paper: see below).
- (ii) migration of genes (and the phenotypic characters that they underpin) between lineages through hybridization, lateral gene transfer, and organelle capture, and;
In addition, the main source of operator bias influencing the resulting topology is a priori homology assessment for morphological data, whereas for molecular data it is selectivity among (i) available characters and (ii) tree-building algorithms. Moreover, both categories of analysis are prone to culling of ‘troublesome’ taxa from matrices, and revised outgroup choices made in search of more ‘intuitively acceptable’ topologies.
Many phylogeneticists advocate a compromise approach to the relative treatment of morphological and molecular characters. In one frequently used protocol, morphological characters are combined with the molecular characters prior to tree building, but only after the initial morphological matrix has been reduced to its bare essentials by culling characters that evoke suspicion, most commonly due to the difficulty of dividing a complex of continuous character into discrete states. However, a recent detailed analysis by Wortley and Scotland (2006) convincingly refutes this approach, demonstrating that the culled characters contain the same average strength of phylogenetic signal as the supposedly superior characters that survive the cull. The alternative, and more commonly used, approach is generally termed ‘mapping’. Here, the morphological characters are placed along the tips of the phylogeny after it has been constructed. Mapping prevents morphological characters from contributing in any way to the tree-building exercise. Mapping can also dissuade researchers from seeking (and then occasionally discovering) new phylogenetically valuable characters. All too often, well-known phenotypic characters of a priori interest are scored and then mapped, thereby effectively generating tautologous interpretations of evolution (Bateman, 1999).
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How significant are optimization and outgroups choice? |
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TopAbstractIntroductionWhat is a flower?Which are the (other)...Which are the benchmark...Which kinds of phylogeny...How significant are optimization...What is the best...What is the best...Do some nodes in...Why is it important...What are the effects...What are the pros...Which key characters best...Why are palaeobotanists obsessed...Are clades such as...Do some categories of...What is the preferred...References |
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The concept of character mapping leads naturally into discussion of another area of phylogenetics that is pivotal to the questions addressed by this paper, namely optimization. If we wish to know what the first flower looked like, but have not found it in the fossil record (such a discovery is highly improbable, given the undoubted patchiness of the fossil record of land-plants), we need to reconstruct that flower conceptually. This is achieved using combinations of characters found in species whose morphology has been carefully described and whose phylogenetic relationships have been rigorously inferred (this phrase is not oxymoronic; it is important to remember that even the most rigorously reconstructed phylogeny remains wholly inferential). Provided we have access to a matrix that thoroughly describes the morphology of all organs of the species under scrutiny, then we can reconstruct the morphology of the hypothetical ancestors that lie on each node of the cladogram. Optimization is most readily achieved by a simple logical protocol that works downward through the tree from the terminal taxa toward the outgroup node (Fig. 3) (e.g. Maddison and Maddison, 2001), though other, more complex, models can be applied, sometimes with advantageous results (Oakley and Cunningham, 2000; Polly, 2001; Webster and Purvis, 2002; Crisp and Cook, 2005).
A most-parsimonious tree, derived from a particular data matrix, yields similar information about the relationships of the coded taxa and the relative lengths of the various branches within the tree, irrespective of whether it is unrooted or rooted. However, an unrooted tree lacks polarity; it cannot be read in terms of transitions from ancestral character states (plesiomorphies) to derived character states (apomorphies). This in turn means that it is not possible to optimize character states in order to reconstruct the hypothetical ancestors occupying the nodes of the tree. In earlier (and more experimental) phases in the evolution of methods of phylogenetic analysis, several conceptually distinct approaches to rooting were explored, but most proved impractical and all appeared at least partially tautologous.
Over the last two decades a single method, termed outgroup comparison (e.g. Nixon and Carpenter, 1993), has become ubiquitous, to the point where it is routinely adopted without serious thought by almost all practising phylogeneticists. It requires the analyst to select a priori a set of comparable taxa (preferably species) that are of interest and are suspected of being an inclusive, monophyletic group (in practice, the strongest guide to perceived monophyly is a previous, and taxonomically broader, phylogenetic analysis; thus, the outgroup method is vulnerable to accusations of logical tautology). Then, one or more additional taxa, thought to lie phylogenetically outside the chosen study group, and hence operationally termed outgroups, are chosen to simultaneously root the tree and polarize the scored characters. If multiple outgroups are chosen they constitute a test (albeit flawed) of the monophyly of the ingroup, since an outgroup taxon that is placed phylogenetically within the ingroup contradicts ingroup monophyly. Clearly, the larger the numbers of ingroup and outgroup taxa, the stronger is this test.
Outgroup choice leaves the analyst with a further quandary. In most cases, the ingroup is chosen because it is a morphologically and/or molecularly distinct aggregate of species, and so is likely to differ considerably from even its phylogenetically closest outgroups (hence, in the resulting trees, a monophyletic ingroup is likely to be subtended by a relatively long branch). These differences make character delimitation more difficult for both morphological and molecular analysts. For the morphologist, the outgroup is likely to lack structures found in the ingroup, possess structures not found in the ingroup, or the two groups may possess structures that are broadly similar yet sufficiently different that their homology cannot be adequately assessed. For the molecular researcher, sequence alignment becomes more challenging for many genic regions, and base saturation becomes an ever-increasing risk. These problems of strong ingroup–outgroup divergence can, in theory, be averted by identifying one or more members of the ingroup as operational outgroups, but the analyst is then imposing a strong subjective overprint on the topology of the resulting tree(s). Certainly, the polarity of characters, and thus the optimizations that allow reconstruction of the properties of the hypothetical ancestor of the ingroup, would be strongly influenced by such a decision.
But before we contemplate implementing of an optimization procedure, we must first select our preferred topology from among the very broad spectrum of land-plant phylogenies generated since 1982.
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What is the best way to choose among the plethora of phylogenies? |
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TopAbstractIntroductionWhat is a flower?Which are the (other)...Which are the benchmark...Which kinds of phylogeny...How significant are optimization...What is the best...What is the best...Do some nodes in...Why is it important...What are the effects...What are the pros...Which key characters best...Why are palaeobotanists obsessed...Are clades such as...Do some categories of...What is the preferred...References |
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One of our primary objectives here is to explore the relative merits of maximizing sampling of taxa versus that of characters per taxon in taxonomically broad (i.e. at least Class level) phylogenetic analyses. Morphological studies that include the best-understood fossils (i.e. conceptual whole plants reconstructed from their component parts: Chaloner, 1986; Bateman, 1992) offer the best opportunity to maximize sampling of taxa that provide strongly contrasting combinations of character states. By contrast, recent molecular trees, some of which compare entire plastid genomes (e.g. Goremykin et al., 2003, 2004, 2005), offer the most obvious means of maximizing the number of characters per taxon.
Given the continuing uncertainties regarding relationships among the major groups of land plants (discussed below), and their potential influence on optimizations of nodes, several branch-points distant from the target node(s), we sought phylogenies that encompassed all such major groups. In the case of morphological phylogenies, no existing study convincingly stretched from the bryophytes to the more derived angiosperms (eudicots sensu APGII: Angiosperm Phylogeny Group, 2003). We therefore took the controversial step of grafting a selected most-parsimonious tree from our recent analysis of 48 lignophytes (angiosperms plus gymnosperms, plus progymnospermous pteridophytes as operational outgroups: Hilton and Bateman, 2006, fig. 10) onto the product of a recent parsimony analysis of 52 coded taxa that focused on pteridophytes but used the fossil non-vascular polysporangiophyte Aglaophyton as outgroup and just five taxa (one progymnosperm plus three primitive pteridospermous gymnosperms and the extant Pinus) as representative ‘placeholders’ for the monophyletic lignophytes (Rothwell and Nixon, 2006, fig. 3). The resulting composite phylogeny contains 95 coded taxa: 47 wholly extinct and 48 containing at least one extant species (Fig. 4).
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Selecting among the many broad-brush molecular trees in order to produce Fig. 5 proved even more problematic. The controversial analysis by Goremykin et al. (2003, 2004; see also Soltis et al., 2004; Martin et al., 2005) stood out as being especially character-rich, since it was based on nearly completely sequenced plastid genomes. The trade-off is that the analysis lacked data from the other two plant genomes (nucleus and mitochondrion), and was restricted to <20 coded taxa; moreover, the taxa were selected as much for their economic importance as their likely phylogenetic significance. This left the trees open to accusations of distortion by long-branch attraction (Soltis et al., 2004; Stefanovic et al., 2004; Leebens-Mack et al., 2005), though a more recent study suggests that likelihood model mis-specification is a more probable source of systematic error in the trees (Goremykin and Hellwig, 2006). The matrix of Soltis et al. (2002) encompassed a similar number of coded taxa, albeit more evenly distributed across the extant land-plant phylogeny, and sequenced eight genic regions distributed among the plastid (rbcL, atpB, psaA, psbB), mitochondrion (mtSSU, cox1, atpA), and nucleus (18S rDNA).
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At the other end of the spectrum of molecular characters per coded taxon are analyses based on a single region but with substantial taxon sampling. A good example is the 2538-taxon rbcL study of land plants by Källersjö et al. (1998, 1999), subsequently reduced to an illuminating series of analyses of various combinations of 80 taxa sampled evenly across the phylogeny of extant land plants by Rydin and Källersjö (2002). Matrices of intermediate dimensions include the 560-taxon, three-region (rbcL, atpB, 18S) analysis of angiosperms by Soltis et al. (2000, 2003a), the 105-taxon five-region (atpB, rbcL, atp1, matR, 18S) analysis of basal angiosperms and gymnosperms by Qiu et al. (2000), and the subsequent 100-taxon, nine-region (atpB, matK, rbcL; atp1, matR, mtSSU, mtLSU; 18S, 26S) analysis of basal angiosperms and gymnosperms by Qiu et al. (2005).
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What is the best way to assess the quality of a phylogeny? |
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TopAbstractIntroductionWhat is a flower?Which are the (other)...Which are the benchmark...Which kinds of phylogeny...How significant are optimization...What is the best...What is the best...Do some nodes in...Why is it important...What are the effects...What are the pros...Which key characters best...Why are palaeobotanists obsessed...Are clades such as...Do some categories of...What is the preferred...References |
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When discussing the reliability of a published phylogeny, three terms are typically employed: accuracy, resolution, and robustness. From our philosophical viewpoint, the term accuracy can legitimately be applied to the topology that reflects the relationships of the taxa analysed only in very rare cases when the analyst is attempting to reconstruct a known and wholly dichotomous genealogy engendered by mankind (e.g. Hillis et al., 1992; Oakley and Cunningham, 2000; contra Rokas and Carroll, 2005). Given that we can never gain access to the ‘one true tree of life’, by definition we cannot assess its accuracy, which is an absolute rather than a relative property.
When a fully dichotomous phylogeny (i.e. one that lacks polytomous nodes) is recovered from the matrix it is often said to be well-resolved. Robustness extends this concept to determining the relative strength of support for a particular node (relationship) within the context of that particular phylogeny. It is traditionally tested using now ubiquitous data-resampling techniques to generate support values, but even strong advocates of these techniques are being obliged to acknowledge their limitations. For example: ‘With high support for their tree, researchers can become confident in incorrect topologies. Although the bootstrap method for assessing confidence was originally suggested to provide confidence intervals for tree branches (i.e. how well the data at hand represent an underlying universe of data), it is now well-recognized that this resampling method and others, such as the jack-knife, provide, at best, a representation of confidence [pertinent] only [to] the data at hand; even random data can yield high bootstrap support. Furthermore, bootstrap values decrease as the number of taxa [included] increases, making it much more likely that high bootstrap values will be obtained if few taxa are analyzed.’ (Soltis et al., 2004, pp. 478–479). In other words, strong statistical support for a particular topology (or, more likely, a set of equally probable topologies)—that is, for a specific hypothesis of relationships—has little bearing on the unknowable property of its accuracy. This conclusion is borne out by numerous studies wherein highly contrasting, yet reliably strongly statistically supported, hypotheses of relationship have been generated from the same substantial data matrix. Such internal contradictions are achieved either by using contrasting tree-building algorithms or by subsampling the matrix; for example, by removing ‘wildcard’ taxa that demonstrably destabilize the topology (an act that often passes unreported in the resulting publications: cf. Hilton and Bateman, 2006), or by omitting specific categories of characters (e.g. third bases in codons: Jeffroy et al., 2006), or both (Philippe, 2006).
If accuracy is unknowable, and robustness unreliable, what criteria are left by which to judge the credibility of a particular inferred phylogeny? Most workers, including ourselves, consider the key word to be congruence. This term was originally coined to describe the relative behaviours of comparable characters (typically morphological features) when simultaneously subjected to a parsimony analysis, which aimed to minimize incongruence among characters (termed homoplasy). But soon incongruence was also used to describe any differences between multiple topologies describing the relationships of the same range of coded taxa.
The latter usage is well illustrated by an insightful, yet infuriating, study on ‘resolving incongruence’ in phylogenetic relationships among eight yeast species by sequencing 106 nuclear genes (
2% of the number present in the genome: Rokas et al., 2003). Despite the small number of taxa analysed, the majority-rule consensus trees generated from each gene collectively offered 20 alternative phylogenetic hypotheses, most rich in ‘strongly supported’ nodes (defined by an arbitrary threshold of a bootstrap value exceeding 70%). Over half of the gene trees required the removal of at least two of the eight species to achieve topological congruence. Moreover, none of the data partitions or statistical patterns explored among the genes allowed the relative performances of individual genes to be predicted or cogently explained. Nonetheless, ‘concatenating’ (combining) all 106 genes ‘yielded a single tree with 100% bootstrap values at every branch’, so the authors ‘conclude[d] that it accurately represents the historical relationships of these eight yeast taxa and will be referred to hereafter as their species tree [they eventually concluded that, on average, 20 genes would generate a reliable species tree]. The maximum support for a single topology regardless of the method of analysis is strongly suggestive of the power of large data sets in overcoming the incongruence present in single-gene analyses’ (Rokas et al., 2003, p. 800). We find this conclusion extraordinary; in our view, the incongruence has not been ‘overcome’ but rather obscured by the sheer volume of data and the failure to explain the cause(s) of the profoundly conflicting phylogenetic signals provided by the individual genes (for a re-evaluation of this data-set see the final section of this paper).
Rather, we are most interested in assessing topological congruence between trees generated from different categories of data, each scored for the same set of taxa (preferably the same species, and ideally the same representative individuals). There is certainly a strong case for comparing phylogenetic signals from the three plant genomes, and from exons and introns; these genic regions operate under strongly contrasting molecular constraints (e.g. Page and Holmes, 1998). Obtaining similar results from all (or at least most) categories of data greatly increases our confidence (in the biological, rather than the statistical, sense) that the relationships recovered are credible. But there is a strong case for analysing genic regions separately before combining them (e.g. Bateman, 1999).
Surely the most versatile category of phylogenetic data is morphology sensu lato. Although restricted in total number of characters, most of those characters are phylogenetically informative (Wortley and Scotland, 2006) and each is potentially divisible into a large number of meaningful character states. Morphology informs not only on phylogenetic relationships but also on function, and through function it directly reflects various modes of natural selection. Detailed knowledge of morphology, along with other biologically relevant data such as symbiotic partners, habitat preference and environmental tolerance, is essential to any evolutionary interpretation of the range of taxa under scrutiny. And morphology maximizes taxon sampling by allowing full integration of fossil species, which serve a vital role in filling the vast morphological and molecular lacunae that separate clades possessing extant representatives.
Thus, the congruence that we seek is similar topologies generated from the same set of taxa by highly contrasting types of data, including morphology. Where trees generated from one or more categories of data (including morphology) disagree with trees generated from the majority of categories, a causal explanation should be sought, based on our knowledge of the biological properties of each category of data. This is the simplest way to identify processes that can confound reliable reconstruction of credible phylogenies.
For molecular data matrices, such processes include lateral gene transfer between taxa (Bergthorsson et al., 2004), lateral gene transfer among the three genomes within a plant (Huang et al., 2005), hybridization (Linder and Rieseberg, 2004), organelle capture (Rieseberg and Wendel, 1993), chromosomally localized gene duplication (Zahn et al., 2005), wholesale gene duplication through polyploidy (De Bodt et al., 2005), lineage sorting (Doyle et al., 1999; Degnan and Rosenberg, 2006), and codon bias. As summarized by Frohlich (2006), codon bias describes substantial differences in the relative frequencies of synonymous codons specifying particular amino acids. It can reflect both mutational biases that affect overall GC content and selection on individual codons (Kawai and Otsuka, 2004; Liu et al., 2004; Liu and Xue, 2005; Jeffroy et al., 2006). Both factors primarily affect third codon positions in general and transitions in particular, and are especially problematic in highly expressed genes. This is because selection among codons is hypothesized to reflect the relative abundances of tRNAs that bear different anticodons but synonymously insert the same amino acid; as a codon becomes more scarce, the synthesis of its protein product is increasingly inhibited. This argument can be used to justify removal of third positions from phylogenetic analyses of highly expressed genes, including typical plastid genes. Such process-based explanations are, in our view, a necessary pre-requisite for selectively removing certain kinds of information from a phylogenetic matrix (see below).
By contrast, morphology can be undermined by convergence toward similar function(s) that is driven by directional or disruptive selection; examples include substantial vegetative modifications associated with transitions from terrestrial to aquatic habitats and from autotrophic to heterotrophic nutrition (e.g. Bateman, 1996), and floral transitions associated with switching pollinators (e.g. Chase, 1999). Less frequently discussed but also problematic are multiple, closely juxtaposed paedomorphic transitions within a clade, where the consequent morphological simplification can under certain circumstances be misconstrued by parsimony as primitiveness rather than as secondary simplification (Bateman, 1996).
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Do some nodes in the land-plant phylogeny merit particular emphasis? |
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TopAbstractIntroductionWhat is a flower?Which are the (other)...Which are the benchmark...Which kinds of phylogeny...How significant are optimization...What is the best...What is the best...Do some nodes in...Why is it important...What are the effects...What are the pros...Which key characters best...Why are palaeobotanists obsessed...Are clades such as...Do some categories of...What is the preferred...References |
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In practice, it is congruence among phylogenetic studies employing contrasting data matrices that has provided a study of land-plant phylogeny with its key reference nodes delimiting major monophyletic groups. Here, we contrast some widely accepted ‘reference nodes’ with other critical areas of land-plant phylogeny that ostensibly carry much greater uncertainty. In order to effectively deploy a bottom-up approach to understanding angiosperm origins, it is necessary to begin the discussion at phylogenetic nodes well below those of greatest interest.
Working upward through a crude consensus phylogeny that is based only on extant groups of land-plants but considering both morphological and molecular analyses (Fig. 2), we immediately encounter the embryophytes, a group that is diagnosed by the presence of archegonia and antheridia and so encompasses all land plants from bryophytes onwards. Excluding the ‘bryophytes’ leaves the monophyletic tracheophytes, which possess bona fide xylem. This is followed by a basal dichotomy within the ‘pteridophytes’<