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Homoplasy and Developmental Constraint: A Model and an Example from Plants1
Abstract
SYNOPSIS. Much attention has been paid to the role of developmental information in estimating phylogenetic relationships and, more recently, to the use of phylog- enies in understanding the evolution of development. At the moment, however, we lack a sufficiently general theory connecting phylogenetic patterns of character evolution to properties of developmental systems. Here we outline a simple model relating homoplasy to the rate of character change and the number of evolvable states, both of which may reflect developmental constraints. Given a particular rate of character change, the fewer the evolvable states the more homoplasy is expected, and vice versa. The repeated evolution of a limited number of forms of bilateral flower symmetry may reflect constraints imposed by overall flower ori- entation and underlying mechanisms of differentiation.
... Multistate character coding is one way to preserve information on the homology relationships between character states (the distinguishable types of a given character) within a phylogenetic data matrix (Strong and Lipscomb, 1999). The number of coded states has been called the evolved, or observed state space, while the number of states that could theoretically be observed has been called the potential, underlying, or evolvable state space (Donoghue and Ree, 2000;Simmons et al., 2004aSimmons et al., , 2004bSteel and Penny, 2005). For example, three distinct petal arrangements are most commonly observed among flowering plants of family Asteridae but a larger variety are theoretically possible, some of which are represented among related lineages (Donoghue and Ree, 2000). ...
... The number of coded states has been called the evolved, or observed state space, while the number of states that could theoretically be observed has been called the potential, underlying, or evolvable state space (Donoghue and Ree, 2000;Simmons et al., 2004aSimmons et al., , 2004bSteel and Penny, 2005). For example, three distinct petal arrangements are most commonly observed among flowering plants of family Asteridae but a larger variety are theoretically possible, some of which are represented among related lineages (Donoghue and Ree, 2000). Multistate characters include morphological characteristics with more than two types (such as the flower shape example), and molecular data types such as DNA and RNA (four states) or amino acids (twenty states) (e.g. ...
... see Felsenstein, 1978;Brandley et al., 2009). Recent studies using computer simulation have tracked the evolution of simulated characters on a "known" phylogenetic tree (Donoghue and Ree, 2000;Simmons et al., 2004aSimmons et al., , 2004b. Such simulations show that characters which can evolve relatively large numbers of states generally undergo less homoplasy than those characters with a smaller evolvable state space (Donoghue and Ree, 2000). ...
... So an alternative cause of homoplasy is required. It has been shown that homoplasy is positively correlated to the limitations on the number of characters states (Donoghue & Ree 2000). Given a particulate rate of evolution (= character change), the fewer the evolvable states the more homoplasy is expected, and vice versa (Donoghue & Ree 2000). ...
... It has been shown that homoplasy is positively correlated to the limitations on the number of characters states (Donoghue & Ree 2000). Given a particulate rate of evolution (= character change), the fewer the evolvable states the more homoplasy is expected, and vice versa (Donoghue & Ree 2000). As shown in other organisms (Wake 1991;Donoghue & Ree 2000), ...
... Given a particulate rate of evolution (= character change), the fewer the evolvable states the more homoplasy is expected, and vice versa (Donoghue & Ree 2000). As shown in other organisms (Wake 1991;Donoghue & Ree 2000), ...
The Astrophorida (Porifera, Demospongiae) currently represent ca 660 extant species worldwide. In tropical and parts of warm temperate waters they are common at quite shallow depths, while in boreal/antiboreal and Arctic waters they are usually deep-water species. They have a very diverse external morphology (massive to thin encrusting, subspherical-, fan-, cupor irregularly-shaped) and display a wide array of external colors. They can be several meters large to a few millimeters thick. However, they all share the same spicule combination: small aster-shaped spicules (microscleres) associated with large four-rayed spicules (megascleres) called triaenes. This unique shared derived character (synapomorphy) is not found in any other Porifera groups. According to the last major morphological revision of the Astrophorida, five families are included in this order: Ancorinidae, Calthropellidae, Geodiidae, Pachastrellidae, and Thrombidae. To date, molecular phylogenetic studies including Astrophorida species are scarce and offer limited sampling. Phylogenetic relationships within this order are therefore for the most part unknown, hypotheses based on morphology largely untested and the spicule evolutionary processes poorly studied. This thesis presents five papers investigating the 1) taxonomy, 2) phylogeny and 3) evolution of the Astrophorida. 1) The first aim of this thesis was to build a molecular phylogeny on solid taxonomical grounds. The three first papers are integrative taxonomical and nomenclatural studies on Atlantic Astrophorida species, notably from the Caribbean coast of Panama and from Norway. In the course of these studies, three species were synonymized, two species were resurrected and two were new to science. This thesis also proposes a list of the North-East Atlantic/Mediterranean Sea Astrophorida species here considered valid. 2) The second aim of this thesis was to investigate the phylogenetic relationships within the Astrophorida with molecular data. The two following papers are molecular phylogeny analyses using a cytochrome c oxidase subunit I (COI) gene partial sequence and the 5’ end terminal part of the 28S rDNA, first considering the Geodiidae alone, then the Astrophorida. Sampling included all five families of this order, three ‘lithistid’ families of Astrophorida affinities as well as two putative Astrophorida (Alectona and Neamphius) still classified today in the Alectonidae, Hadromerida. The COI and 28S (C1-D2) datasets were concatenated in a single matrix containing a total of 152 taxa (29 genera, 2 sub-genera, 89 species) and 1,527 characters. The resulting tree showed that i) the Astrophorida was monophyletic, ii) the sub-orders Euastrophorida and Streptosclerophorida were both found polyphyletic, iii) the Calthropellidae were monophyletic (and found to be a subfamily of the Geodiidae), iv) the Geodiidae, the Ancorinidae and the Pachastrellidae appeared polyphyletic and had to be redefined, v) a new subfamily of the Geodiidae was revealed (Caminellinae subfam. nov.) and finally vi) some genera were found to be polyphyletic (Ecionemia, Erylus, Poecillastra, Penares, Rhabdastrella, Stelletta and Vulcanella). Based on these results, a revised classification of the Astrophorida is proposed, along with a key to the families, sub-families and incertae sedis. The use of a phylogenetic classification of the Astrophorida (following the principles of phylogenetic nomenclature and the rules of the PhyloCode) was also explored. 3) The third aim of this thesis was to investigate the evolution of Astrophorida sponge spicules, particularly diverse in this order. In the two last papers, spicule categories were mapped on the molecular phylogenetic trees. The main result was that spicule homoplasy is more common than what we expected: convergent evolution and secondary losses have happened many times, in all the clades, for megascleres and microscleres. The implications of these results are discussed with respect to the function of spicules, their evolution and the taxonomy of sponges.
... Malpighiaceae provide a natural test of the role of intrinsic versus extrinsic factors in generating morphological stasis; this is particularly relevant in the context of Anderson's earlier hypothesis outlined above, but also more generally in the context of developmental constraints that have been hypothesized to limit floral form (18). The evolution of floral symmetry within the large asterid clade, which includes snapdragons and mints, is highly homoplastic, but a limited subset of the possible floral forms are found to occur, most of which have five corolla lobes, two dorsal (adaxial) petals, and a medially positioned ventral (abaxial) petal (18). ...
... Malpighiaceae provide a natural test of the role of intrinsic versus extrinsic factors in generating morphological stasis; this is particularly relevant in the context of Anderson's earlier hypothesis outlined above, but also more generally in the context of developmental constraints that have been hypothesized to limit floral form (18). The evolution of floral symmetry within the large asterid clade, which includes snapdragons and mints, is highly homoplastic, but a limited subset of the possible floral forms are found to occur, most of which have five corolla lobes, two dorsal (adaxial) petals, and a medially positioned ventral (abaxial) petal (18). Although developmental constraint has been invoked to explain these findings, this hypothesis has not been critically tested. ...
... 8)] have maintained bilaterally symmetrical corollas, but the flowers have been reoriented such that they display two dorsal (adaxial) petals and a ventrally positioned medial petal that may serve as a landing platform, rather than a single dorsal banner petal and no clear landing platform. Although such reorientations appear to be rare across angiosperms (18), they may be more readily accomplished in Malpighiaceae, where two dorsal petal primordia are the norm early in development and the dorsal medial position of the mature banner petal appears to be achieved by a twisting of the flower stalk later in development (23). Indeed, recent developmental genetic studies (38)(39)(40) have shown that the expression of CYCLOIDEA2-like (CYC2-like) genes, which are responsible for establishing floral symmetry in a wide range of angiosperms, has been altered in Malpighiaceae. ...
Significance
Long-term morphological stasis is a major feature of the paleontological record, but the explanation for this pattern has been controversial. Here, we use the species-rich plant clade Malpighiaceae to determine whether long-term floral stasis is maintained by selection or developmental and genetic constraint. Our results, which use an explicit phylogenetic framework and comparative methods, strongly support selection. We hypothesize that this floral morphology has been maintained over tens of millions of years via their specialized pollinator interaction with oil-collecting bees. To our knowledge, this study in which stasis has been connected to such a plant-pollinator mutualism, is unique, and opens the door to future research on how this association may have enhanced diversification in this plant lineage.
... Convergent evolution generally defines phylogenetic patterns wherein similar phenotypes are observed in species that do not share a recent common ancestor, which is often attributed to common selective pressures in distantly related lineages (Mahler et al., 2017;Stayton, 2015;Wake et al., 2011). Furthermore, character evolution models predicted a higher probability of convergence in species groups (clades) that feature somewhat invariable morphological traits (Bock, 1963;Donoghue & Ree, 2000). Although evolution generally proceeds via the rearrangement of preexisting morphologies, not all organismal structures are free to vary (Bock, 1959;Frazzetta, 1976;Wainwright, 2007). ...
... The potential for traits to evolve (evolvability) might be constrained by the inherited ancestral state of a clade (Bock, 1963;Donoghue & Ree, 2000;Losos, 2011). Evolution may therefore follow predictable trajectories within the bounds of an ancestral architecture, though ...
Synopsis
Species groups that feature traits with a low number of potentially variable (evolvable) character states are more likely to repeatedly evolve similar phenotypes, that is, convergence. To evaluate this phenomenon, this present paper addresses anatomical alterations in turtles that convergently evolved shell kinesis, for example, the movement of shell bones to better shield the head and extremities. Kinesis constitutes a major departure from the evolutionarily conserved shell of modern turtles, yet it has arisen independently at least 8 times. The hallmark signature of kinesis is the presence of shell bone articulations or “hinges,” which arise via similar skeletal remodeling processes in species that do not share a recent common ancestor. Still, the internal biomechanical components that power kinesis may differ in such distantly related species. Complex diarthrodial joints and modified muscle connections expand the functional boundaries of the limb girdles and neck in a lineage-specific manner. Some lineages even exhibit mobility of thoracic and sacral vertebrae to facilitate shell closure. Depending on historical contingency and structural correlation, a myriad of anatomical alterations has yielded similar functional outcomes, that is, many-to-one mapping, during the convergent evolution of shell kinesis. The various iterations of this intricate phenotype illustrate the potential for the vertebrate musculoskeletal system to undergo evolutionary change, even when constraints are imposed by the development and structural complexity of a shelled body plan. Based on observations in turtles and comparisons to other vertebrates, a hypothetical framework that implicates functional interactions in the origination of novel musculoskeletal traits is presented.
... The extent of the relationship between biological features and phylogenetic distance has also been much discussed in the context of the 'morphology and molecules' debate (Hillis, 1987;Patterson et al., 1993;Scotland et al., 2003;Wiens, 2004) as well as the extent of convergence and homoplasy across the tree of life (Sanderson & Donoghue, 1996;Donoghue & Ree, 2000;Wake et al., 2011). Although these discussions have led to divided opinions, it is most widely accepted to use DNA sequence data to infer phylogenetic trees (Felsenstein, 1978(Felsenstein, , 2004Hillis et al., 1994;Hillis, 1995;Posada & Crandall, 1998). ...
... Lower global correlations are more common in the binary datasets than in the multistate datasets. This is probably due to the increased likelihood of observing homoplasy in binary characters for a given rate of state change (Donoghue & Ree, 2000). However, even for multistate characters, a global correlation of less than 0.5 is observed in 34% of all matrices (for illustrative purposes, a global correlation of 0.5 is midway between Fig. 3c,d). ...
AimPhylogenetic trees provide a framework for understanding the evolution of features (properties, characters or traits) of species, where closely related species share many common or similar features. This property of phylogenetic trees has practical use in applications such as bio-prospecting, where an optimal strategy exploits phylogenetic information to target closely related species to search for shared features of interest. The implicit corollary of this is that distantly related species share few features in common. This property of phylogenetic trees is thought to be useful for conservation evaluation in choosing sets of species that maximize the present utilitarian benefits of extant feature diversity (such as biologically active compounds or source systems for genetic engineering) as well as maximizing the range of evolutionary trajectories into the future. LocationGlobal. Methods
Here, we investigate the relationship between phylogenetic trees and biological features through both simulation and meta-analysis of 223 publicly available feature matrices. ResultsWe demonstrate that phylogenetic tree distance, both in real and simulated datasets, is correlated with feature similarity only for a short relative distance along the tree, such that there is no relationship for the majority of the length of most phylogenetic trees. In other words, close relatives share more features than distant relatives but beyond a certain threshold increasingly more distant relatives are not more divergent in phenotype. Main conclusionsMeasures of phylogenetic diversity based upon maximizing phylogenetic distance may not maximize feature diversity.
... A link between evolutionary flexibility and homoplasy has been suggested by several authors (e.g. Chapman et al., 1979; Lamboy, 1994; Naylor and Kraus, 1995; Donoghue and Ree, 2000; Simmons et al., 2004). However, evidence for a negative correlation between states per character and homoplasy (among character data in which the number of steps was free to vary) has been based on evolutionary simulations employing the consistency index as the homoplasy metric (Lamboy, 1994; Donoghue and Ree, 2000). ...
... Chapman et al., 1979; Lamboy, 1994; Naylor and Kraus, 1995; Donoghue and Ree, 2000; Simmons et al., 2004). However, evidence for a negative correlation between states per character and homoplasy (among character data in which the number of steps was free to vary) has been based on evolutionary simulations employing the consistency index as the homoplasy metric (Lamboy, 1994; Donoghue and Ree, 2000). The ci distributions generated fall within a range of values for which change in the amount of homoplasy that may be measured, rather than a decrease in the number of homoplastic state changes, presents an alternative explanation for the negative correlation observed. ...
To identify a biological signal in the distribution of homoplasy, it is first necessary to isolate non-biological factors affecting its measurement. The number of states per character in a phylogenetic data matrix may indicate evolutionary flexibility and, consequently, the likelihood of recurrent evolution. However, we show here that the number of states per character limits the maximum number of steps that may be inferred using parsimony. A formula is provided for the maximum number of steps that may be taken by a character with a given number of states and taxa. We show that as more character states are included the maximum proportion of steps that can be attributed to homoplasy falls, and the greatest amount of homoplasy measurable with the consistency index declines.
© The Willi Hennig Society 2009.
... Earlier comparative evaluations of floral patterns, especially in eudicots, have focused mainly on the perianth rather than the stamens (e.g. Donoghue et al. , 1998;Donoghue & Ree, 2000), but a more complete picture may be obtained by including the stamens, especially in monocots, in which both stamens and tepals are typically differentiated into two distinct whorls. ...
... Asterid eudicots have also experienced repeated evolution of a limited number of forms of bilateral flower symmetry (e.g. Coen & Nugent, 1994;Donoghue et al., 1998;Endress, 1999), similarly reflecting constraints imposed by floral orientation and differentiation (Donoghue & Ree, 2000). In the wild-type flower of the 'model' organism Antirrhinum the adaxial stamen is suppressed, and the perianth whorl is clearly differentiated into upper (adaxial) and lower (abaxial) lips of two and three petals, respectively (Fig. 1c) (equivalent to our Pattern 1, although here there is no differentiation of inner and outer stamen whorls). ...
Summary 25
Acknowledgements 42
References 42
Here we explore morphological transitions among monocot flowers and discuss them in terms of modification of existing structures. Monocot flowers are typically arranged in five whorls (carpels, inner and outer stamens, inner and outer tepals), and are radially symmetrical, constructed around a 3-fold axis of rotational symmetry that delineates three planes of bilateral symmetry. Differential development of one or two of the three organs within a whorl inevitably emphasizes one plane of symmetry, by eliminating the other planes, rendering the whorl zygomorphic. Zygomorphy (monosymmetry) has evolved more than once in monocotyledons. Stamen suppression is a widespread aspect of zygomorphy and conforms to two broad categories of pattern. In the more frequent Pattern 1, 1–3(−5) adaxial stamens (both inner and outer) are either reduced in size or entirely suppressed. Pattern 2 involves loss, reduction or modification of at least the outer abaxial stamen. Pattern 2 often characterizes groups that are phylogenetically embedded within Pattern 1 clades, perhaps indicating that this pattern results from loss of function or overexpression of the same genes involved in establishment of Pattern 1. Heterotopy has been an important evolutionary phenomenon among Zingiberales (some stamens becoming petaloid) and perhaps grasses (petals possibly becoming sepaloid). Heterochrony is the most frequent cause of more subtle changes in the degree of bilateral symmetry shown by monocot flowers by enhancing (peramorphosis) or retarding (paedomorphosis) individual organs within specific whorls.
... In morphological character based tree, the association among the tribes as well as genera was not clear whereas these associations were resolved in molecular tree. The reason may be the large number of characters, low level of homoplasy and relative unambiguity in scoring method of molecular data (Michael & Richard, 2000;James & Kenneth, 1994;) that may help in representing the clear picture of the relationships. Based on molecular data, within Solanoideae five tribes, Datureae, Solaneae, Lycieae, Capsiceae, and Physaleae were observed whereas morphological data also established existence of these tribes however, their association was not conclusive. ...
... Although this effect is understood to affect molecular data, discrete morphological datasets may possess increased susceptibility to this effect because of the frequent use of binary character coding schemes. Discrete characters constrained to fewer states increases signal loss at high evolutionary rates due to increased levels of homoplasy, saturation, and lower information content overall (Donoghue and Ree 2000). The extent to which continuous traits are constrained in their evolution on average is not well understood. ...
During the modern synthesis, researchers merged insights from natural history, evolutionary genetics, and paleontology to develop a cohesive theoretical foundation for evolutionary theory. Since then, the rapid emergence of genomic resources has revolutionized our understanding of evolutionary processes. Despite neontological successes, paleobiology has lagged behind, due in part to perceived challenges in collecting and analyzing morphological data. As a result, the earlier synthetic evolutionary view developed between neo- and paleontology has not kept pace with the current data-centric landscape. To address these issues, I aim to integrate morphological data representing fossil and living taxa into the modern evolutionary framework through the development of novel statistical approaches that leverage sources of data previously thought to be unconventional. These developments follow two main threads: 1) development of a statistical framework through which to infer phylogeny among fossil taxa by merging increasingly large and high-throughput quantitative morphological datasets with stratigraphic information, and 2) developing empirical applications of new approaches to comprehensively examine long-hypothesized but under-studied patterns in evolutionary rate throughout time, and mosaic change by integrating morphological, stratigraphic, and developmental data.
... Ratchetlike mechanisms have also been posited for morphological evolution, for example, Dollo's Law [6], which posits that a complex trait, once lost, cannot be regained. It has also been suggested that certain characteristics may reduce the ability to attain other states [7][8][9], with the ultimate result that extreme specialization will not only limit a clade's 'evolvability' (potential morphological diversity) but also their ability to adapt to environmental disturbances [10,11]. ...
Large carnivorous mammals have been suggested to show a ratchet-like mode of morphological evolution. A limited number of specializations for hypercarnivory evolve repeatedly in multiple clades, with those lineages evolving such specialities being unable to retreat back along their evolutionary trajectory or jump between adaptive peaks. While it has been hypothesized that such mechanisms should have applied to the evolution of other terrestrial carnivores, the non-mammalian synapsid clade Therocephalia appears to defy this expectation. The earliest, basalmost members of this clade are large macropredators, and it is later that small carnivores appear, seemingly evolving from top-predator ancestors. In order to test this reading of therocephalian evolution, variation in rates of body size evolution were tested for and incorporated into an ancestral reconstruction. Similar studies were made of the evolution of discrete characters related to carnivory. All analyses indicate the ancestral therocephalian was a large macro-predator, with serrated teeth, elongated canines and robust lower jaws. Small sizes apparently evolve later. It is therefore suggested that the hypercarnivore ratchet is a feature of mammalian evolution.
... Although the role of natural selection is central to explaining convergent evolution (but see [12,13]), developmental processes may ultimately limit the number of evolvable character states [3]. For instance, the likelihood of trait convergence might be higher in species groups that exhibit morphological stasis owing to design limitations imposed by underlying developmental processes [14,15]. The atypical turtle body plan is an outstanding model to examine such a phylogenetic pattern [16,17]. ...
Understanding developmental processes is foundational to clarifying the mechanisms by which convergent evolution occurs. Here, we show how a key convergently evolving trait is slowly ‘acquired’ in growing turtles. Many functionally relevant traits emerge late in turtle ontogeny, owing to design constraints imposed by the shell. We investigated this trend by exam- ining derived patterns of shell formation associated with the multiple (at least 8) origins of shell kinesis in small-bodied turtles. Using box turtles as a model, we demonstrate that the flexible hinge joint required for shell kin- esis differentiates gradually and via extensive repatterning of shell tissue. Disproportionate changes in shell shape and size substantiate that this trans- formation is a delayed ontogenetic response (3–5 years post-hatching) to structural alterations that arise in embryogenesis. These findings exem- plify that the translation of genotype to phenotype may reach far beyond embryonic life stages. Thus, the temporal scope for developmental origins of adaptive morphological change might be broader than generally understood. We propose that delayed trait differentiation via tissue repat- terning might facilitate phenotypic diversification and innovation that otherwise would not arise due to developmental constraints.
... Recent molecular studies have found that genetic convergence underlies many homoplastic phenotypes, which suggests that developmental mechanisms are indeed constrained ( Shubin et al., 2009 ;Christin et al., 2010 ;Rosenblum et al., 2014 ). One eff ective approach that illuminates the role of development in shaping morphological diversity is to characterize and compare the underlying processes of development of the homoplastic traits ( Donoghue and Ree, 2000 ;Wake et al., 2011 ). ...
Premise of the study:
Observations of floral ontogeny indicated that floral organ initiation in pentapetalous flowers most commonly results in a median-abaxial (MAB) petal during early development, a median-adaxial (MAD) petal being less common. Such different patterns of floral organ initiation might be linked with different morphologies of floral zygomorphy that have evolved in Asteridae. Here, we provide the first study of zygomorphy in pentapetalous angiosperms placed in a phylogenetic framework, the goal being to find if the different patterns of floral organ initiation are connected with particular patterns of zygomorphy.
Methods:
We analyzed patterns of floral organ initiation and displays of zygomorphy, extracted from floral diagrams representing 405 taxa in 330 genera, covering 83% of orders (30 out of 36) and 37% of families (116 out of 313) in core eudicots in the context of a phylogeny using ancestral state reconstructions.
Key results:
The MAB petal initiation is the ancestral state of the pattern of floral organ initiation in pentapetalous angiosperms. Taxa with MAD petal initiation represent ∼30 independent origins from the ancestral MAB initiation. There are distinct developmental processes that give rise to zygomorphy in different lineages of pentapetalous angiosperms, closely related lineages being likely to share similar developmental processes.
Conclusions:
We have demonstrated that development indeed constrains the processes that give rise to floral zygomorphy, while phylogenetic distance allows relaxation of these constraints, which provides novel insights on the role that development plays in the evolution of floral zygomorphy.
... Although this effect is understood to affect molecular data, discrete morphological data sets may possess increased susceptibility to this effect because of the frequent use of binary character coding schemes. Discrete characters constrained to fewer states increases signal loss at high evolutionary rates due to increased levels of homoplasy, saturation, and lower information content overall (Donoghue and Ree 2000). The extent to which continuous traits are constrained in their evolution on average is not well understood. ...
The recent surge in enthusiasm for simultaneously inferring relationships from extinct and extant species has reinvigorated interest in statistical approaches for modelling morphological evolution. Current statistical methods use the Mk model to describe substitutions between discrete character states. Although representing a significant step forward, the Mk model presents challenges in biological interpretation, and its adequacy in modelling morphological evolution has not been well explored. Another major hurdle in morphological phylogenetics concerns the process of character coding of discrete characters. The often subjective nature of discrete character coding can generate discordant results that are rooted in individual researchers' subjective interpretations. Employing continuous measurements to infer phylogenies may alleviate some of these issues. Although not widely used in the inference of topology, models describing the evolution of continuous characters have been well examined, and their statistical behaviour is well understood. Also, continuous measurements avoid the substantial ambiguity often associated with the assignment of discrete characters to states. I present a set of simulations to determine whether use of continuous characters is a feasible alternative or supplement to discrete characters for inferring phylogeny. I compare relative reconstruction accuracy by inferring phylogenies from simulated continuous and discrete characters. These tests demonstrate significant promise for continuous traits by demonstrating their higher overall accuracy as compared to reconstruction from discrete characters under Mk when simulated under unbounded Brownian motion, and equal performance when simulated under an Ornstein-Uhlenbeck model. Continuous characters also perform reasonably well in the presence of covariance between sites. I argue that inferring phylogenies directly from continuous traits may be benefit efforts to maximise phylogenetic information in morphological datasets by preserving larger variation in state space compared to many discretisation schemes. I also suggest that the use of continuous trait models in phylogenetic reconstruction may alleviate potential concerns of discrete character model adequacy, while identifying areas that require further study in this area. This study provides an initial controlled demonstration of the efficacy of continuous characters in phylogenetic inference.
... Convergence also provides insights into the relative evolutionary accessibility of certain phenotypes and how structural features of organisms may influence their evolutionary response (Sanderson and Hufford 1996;Donoghue and Ree 2000;Christin et al. 2013). The degree to which a particular character repeatedly emerges must be a function of both the pervasiveness of the selection pressure(s) and the relative ease of its evolution. ...
The deciduous habit of northern temperate trees and shrubs provides one of the most obvious examples of convergent evolution, but how did it evolve? Hypotheses based on the fossil record posit that deciduousness evolved first in response to drought or darkness and preadapted certain lineages as cold climates spread. An alternative is that evergreens first established in freezing environments and later evolved the deciduous habit. We monitored phenological patterns of 20 species of Viburnum spanning tropical, lucidophyllous (subtropical montane and warm temperate), and cool temperate Asian forests. In lucidophyllous forests, all viburnums were evergreen plants that exhibited coordinated leaf flushes with the onset of the rainy season but varied greatly in the timing of leaf senescence. In contrast, deciduous species exhibited tight coordination of both flushing and senescence, and we found a perfect correlation between the deciduous habit and prolonged annual freezing. In contrast to previous stepwise hypotheses, a consilience of independent lines of evidence supports a lockstep model in which deciduousness evolved in situ, in parallel, and concurrent with a gradual cooling climate. A pervasive selective force combined with the elevated evolutionary accessibility of a particular response may explain the massive convergence of adaptive strategies that characterizes the world’s biomes.
... In the same way, the paraphyly of C. cornuta and C. cubensis is likely owed to a taxonomy informed by misleading morphological similarities. Similar conflicts between molecular and morphological differentiation have been documented in numerous lineages of animals and plants (Foote, 1993;Mayr, 2011) and can be explained by developmental (Erwin, 2007;Wake et al., 2011) and ecological (Donoghue & Ree, 2000) constraints on morphology. Thus, we assume that morphological uniformity is masking bryophyte radiations. ...
Aim
How disjunct distributions arise and why organisms differ in diversification patterns remain some of the most compelling fundamental questions in biogeography. We carry out phylogeographical analyses of the pantropical liverwort genus Ceratolejeunea to identify its geographical origin and the dispersal routes by which it gained its Neotropical‐African disjunction. Furthermore, we investigate whether there is geographical structure in Ceratolejeunea on islands and whether island diversity is a result of radiations or recurrent migration.
Location
America, Africa and Australasia.
Methods
Sequences of two chloroplast regions ( trnL – F , rbcL ) and the nuclear ribosomal ITS region were obtained for 55 accessions of 20 species to explore the phylogeny, divergence times and ancestral areas of Ceratolejeunea . The phylogeny was reconstructed using maximum likelihood and Bayesian inference approaches, and divergence times were estimated with a Bayesian relaxed clock method and fossil and secondary calibrations. Ancestral areas were estimated using BioGeo BEARS.
Results
Ceratolejeunea likely originated in the Neotropics during the Palaeogene (42.2 Ma, 95% HPD : 22.2–64.8) and the initial diversification of its crown group took place between the Eocene and Miocene (25.5 Ma, 95% HPD : 16.6–35.8). Although boreotropical migration and subsequent extinction in northern regions cannot be rejected, the observed disjunctions are best explained by four transoceanic dispersal events from the Neotropics to Africa during the late Oligocene to Pleistocene. Geographical structure is prevalent on islands, particularly in the C . cornuta complex. Three species and the subgenus Ceratolejeunea are recovered as paraphyletic.
Main conclusions
Widespread paraphyly and sister group relationships between disjunct taxa indicate an important role of cryptic speciation and transoceanic dispersal with subsequent genetic differentiation in the evolution of Ceratolejeunea . On islands, recurrent migration, rather than radiation, has shaped bryophyte diversity.
... A subsequent paired t-test of the residual CI values from this model revealed no significant difference (t = 0.917, P = 0.362) between craniodental and postcranial partitions. We note that other variables have been demonstrated empirically to influence CI (Donoghue and Ree 2000;Hoyal Cuthill et al. 2010). HER values (Archie 1989(Archie , 1996Archie and Felsenstein 1993) were similar in the craniodental (x = 0.582) and postcranial skeleton (x = 0.571; paired t = 0.621, P = 0.537). ...
... A subsequent paired t-test of the residual CI values from this model revealed no significant difference (t = 0.917, P = 0.362) between craniodental and postcranial partitions. We note that other variables have been demonstrated empirically to influence CI (Donoghue and Ree 2000;Hoyal Cuthill et al. 2010). HER values (Archie 1989(Archie , 1996Archie and Felsenstein 1993) were similar in the craniodental (x = 0.582) and postcranial skeleton (x = 0.571; paired t = 0.621, P = 0.537). ...
Morphological cladograms of vertebrates are often inferred from greater numbers of characters describing the skull and teeth than from postcranial characters. This is either because the skull is believed to yield characters with a stronger phylogenetic signal (i.e., contain less homoplasy), because morphological variation therein is more readily atomized, or because craniodental material is more widely available (particularly in the palaeontological case). An analysis of 85 vertebrate datasets published between 2000 and 2013 confirms that craniodental characters are significantly more numerous than postcranial characters, but finds no evidence that levels of homoplasy differ in the two partitions. However, a new partition test based on tree-to-tree distances (as measured by Robinson Foulds metric) rather than tree length reveals that relationships inferred from the partitions are significantly different about one time in three, much more often than expected. Such differences may reflect divergent selective pressures in different body regions, resulting in different localized patterns of homoplasy. Most systematists attempt to sample characters broadly across body regions, but this is not always possible. We conclude that trees inferred largely from either craniodental or postcranial characters in isolation may differ significantly from those that would result from a more holistic approach. We urge the latter. This article is protected by copyright. All rights reserved
... For some character types, the number of possible character states may be relatively easy to establish, such as four states for DNA or RNA, 20 states for standard amino acids and two states for binary (presence/absence) morphological characters. However, for most multistate morphological characters, the number of possible states is essentially unknown [1]. Most phylogenetic reconstruction methods treat morphological characters much like molecular data and implicitly assume that the potential state space is finite for a given character. ...
Biological variety and major evolutionary transitions suggest that the space of possible morphologies may have varied among lineages and through time. However, most models of phylogenetic character evolution assume that the potential state space is finite. Here, I explore what the morphological state space might be like, by analysing trends in homoplasy (repeated derivation of the same character state). Analyses of ten published character matrices are compared against computer simulations with different state space models: infinite states, finite states, ordered states and an ‘inertial’ model, simulating phylogenetic constraints. Of these, only the infinite states model results in evolution without homoplasy, a prediction which is not generally met by real phylogenies. Many authors have interpreted the ubiquity of homoplasy as evidence that the number of evolutionary alternatives is finite. However, homoplasy is also predicted by phylogenetic constraints on the morphological distance that can be traversed between ancestor and descendent. Phylogenetic rarefaction (sub-sampling) shows that finite and inertial state spaces do produce contrasting trends in the distribution of homoplasy. Two clades show trends characteristic of phylogenetic inertia, with decreasing homoplasy (increasing consistency index) as we sub-sample more distantly related taxa. One clade shows increasing homoplasy, suggesting exhaustion of finite states. Different clades may, therefore, showdifferent patterns of character evolution. However, when parsimony uninformative characters are excluded (which may occur without documentation in cladistic studies), it may no longer be possible to distinguish inertial and finite state spaces. Interestingly, inertial models predict that homoplasy should be clustered among comparatively close relatives (parallel evolution), whereas finite state models do not. If morphological evolution is often inertial in nature, then homoplasy (false homology) may primarily occur between close relatives, perhaps being replaced by functional analogy at higher taxonomic scales. © 2015 The Author(s) Published by the Royal Society. All rights reserved.
... The estimation of phylogenetic signal may be affected by the limitations of the existing methods, the inaccuracy of the phylogenetic estimate, or by errors in the data itself [72], which may explain the apparent inconsistency of our results that show phylogenetic signal using homoplasious characters. Other factors that may affect this interpretation include errors in the characterization and coding of the character states [73]. However, other authors consider that phylogenetic signal may not be associated with evolutionary rates, and recommend that phylogenetic signal should not be used to make interpretations about evolutionary processes [74]. ...
Miconieae is the largest tribe in the Melastomataceae with over 1,850 species. The members of Miconieae display a wide range of morphological diversity, and seed morphology is no exception. Previous studies have found that seed morphological diversity is not congruent with traditional classifications, and suggest that it may reflect evolutionary relationships within Miconieae. Here we characterize seed morphology of 364 species of Miconieae. The morphological data set and a DNA sequence data matrix were analyzed under a parsimony and Bayesian framework. Seed characters were used to test taxonomic and clade hypotheses, to estimate morphological ancestral character states, and to assess phylogenetic signal. The phylogenetic analyses of morphological data retrieved a poorly-resolved, low-supported phylogeny; in contrast, a relatively strongly supported phylogeny was estimated using the molecular data. Hypothesis testing procedures could only reject the monophyly of Clidemia, Leandra, and Miconia. The results indicated that the seed morphological characters were homoplasious, but contained phylogenetic signal. The morphological seed types that were described in previous studies did not support any of the clades retrieved by the molecular phylogeny. In contrast with previous investigations, our study shows that although seed morphology is very variable, it does not provide information for supporting some genera or clades within Miconieae. However, it is suggested that seed characters in combination with other vegetative and reproductive traits may aid in the characterization of smaller clades. The presence of phylogenetic signal retrieved by homoplasious characters may indicate that diversification of seed characters could have an adaptive component. Further studies that increase taxon sampling, refine seed trait characterization, and evaluate the alleged relationships between environmental variables and seed diversification will contribute to a better understanding of seed morphology and evolution in this species-rich tribe.
... There is also a small amount of differentiation of the other corallites in Isopora colonies, sufficient to separate them as radial corallites. For plants, it has been proposed that apparent convergences of some characters may actually be indicative of deep ancestral programming within a clade, which places constraints on the way in which variations can be formed in clade members: characters or character states might re-appear in combination with a different set of other characters (Donoghue and Ree 2000; Donoghue 2005).The presence of an axial corallite, now seen first in Astreopora and later in Acropora and Isopora, may be a parallelism in the sense described by Donoghue (2005; also quoting from Gould 2002), that is, it results from " historical constraints in the evolving system—the same condition originates again and again within a lineage owing to something about the structure and development of the shared ancestor " . A similar parallelism may also apply to the dendritic branching in A. cenderawasih sp. ...
Nuwei Vivian Wei, Hernyi Justin Hsieh, Chang-Feng Dai, Carden C. Wallace, Andrew H. Baird, and Chaolun Allen Chen (2012) Reproductive isolation among Acropora species (Scleractinia: Acroporidae) in a marginal coral assemblage. Zoological Studies 51(1): 85-92. Hybridization was proposed as being an important source of evolutionary novelty in broadcast-spawning reef-building corals. In addition, hybridization was hypothesized to be more frequent at the periphery of species' ranges and in marginal habitats. We tested the potential for hybridization in 2 ways: observations of the time of spawning and non-choice interspecific fertilization experiments of 4 sympatric Acropora species in a non-reefal coral assemblage at Chinwan Inner Bay (CIB), Penghu Is., Taiwan. We found that colonies of more than 1 species rarely released gametes at the same time, thus limiting the opportunities for cross-fertilization in the wild. On the few occasions when different species released gametes in synchrony, interspecific fertilization in experimental crosses was uniformly low (the proportion of eggs fertilized ranged 0%-4.58% with a mode of 0%), and interspecific-crossed embryos ceased development and died within 12 h after initially being fertilized. Ecological and experimental analyses indicated that reproductive isolation exists in these 4 Acropora species even though they have the opportunities to spawn synchronously, suggesting that hybridization is not very frequent in this marginal coral habitat at CIB. http://zoolstud.sinica.edu.tw/Journals/51.1/85.pdf
... Gould was not just a rhetorical advocate of constraint but himself carried out extensive empirical studies, especially on the West Indian land snail genus Cerion, in which he described a tradeoff relationship between whorl size and whorl number that results from coiling and growth allometry (Gould 1989). Other conceptual treatments elaborated constraint theory (Maynard-Smith et al. 1985;Zelditch et al. 1993), and further empirical evidence was provided by comparative morphology (Bell 1987;Vogl and Rienesl 1991;Caldwell 1994), experimental embryology (Alberch and Gale 1985;Webb 1989;Streicher and Müller 1992), plant biology (Donoghue and Ree 2000), quantitative genetics (Cheverud 1984;Rasmussen 1987;Wagner 1988), and genomics (Roux and Robinson-Rechavi 2008). ...
In evolutionary biology, the term “spandrel” infallibly elicits the memory of Steve Gould. It has become a standard in referring to constructional byproducts and developmental constraints. More often than not, these were regarded as lesser facets of evolutionary change, with priority given to population dynamics and the workings of natural selection. But the fundamental criticism, in the spandrels paper and other works of Gould, of the absence of organism level factors in the standard Modern Synthesis account, also helped trigger the EvoDevo revolution and important reconceptualizations of evolutionary theory. Recent versions of theory expansion include many of Gould’s propositions but also theoretical changes emerging from other fields, such as genomics, non-genetic inheritance, niche construction, and others. These amount not merely to a numerical addition of factors to be taken into account, but also initiate major shifts in theory structure. As a consequence, today’s extended frameworks of evolutionary theory entail a significant increase in explanatory capacity and predictive power.
... For plants, it has been proposed that apparent convergences of some characters may actually be indicative of deep ancestral programming within a clade, which places constraints on the way in which variations can be formed in clade members: characters or character states might re-appear in combination with a different set of other characters (Donoghue and Ree 2000;Donoghue 2005).The presence of an axial corallite, now seen first in Astreopora and later in Acropora and Isopora, may be a parallelism in the sense described by Donoghue (2005; also quoting from Gould 2002), that is, it results from "historical constraints in the evolving system-the same condition originates again and again within a lineage owing to something about the structure and development of the shared ancestor". A similar parallelism may also apply to the dendritic branching in A. cenderawasih sp. ...
Three new species of Astreopora (Hexacorallia: Scleractinia: Acroporidae), from Cenderawasih Bay in West Papua, exhibit morphological innovations for this conservative genus, extant since the Cretaceous. Two species are fully branching, a condition never previously described for Astreopora: Astreopora cenderawasih sp. nov. has dendritic branching, also seen in the confamilial genus Montipora, whereas branches of A. acroporina sp. nov. possess an axial corallite, regarded as the key morphological innovation facilitating rapid diversification and dominance of reefs in the younger, confamilial and most diverse genus Acropora (staghorn corals). We propose that these novel characters may be parallelisms indicating deep familial homologies. The third species, Astreopora montiporina sp. nov., has expansive coenosteum, reminiscent of plating Montipora. The new species form part of the most species-rich Astreopora assemblage reported to date, comprising 14 species. The unique tectonic and eustatic history of Cenderawasih Bay may have played a role in the evolution of these new species.
... Instead of accumulating new character states as new lineages arise, the number of character states appears to be constrained in most empirical data sets (Wagner, 2000). Constraints on design arising from development or function can thus result in homoplasy, as species end up sharing character states that are not inherited from their most recent common ancestor (Sanderson & Donoghue, 1989; Wake, 1991; Donoghue & Ree, 2000; Masters, 2007). This leads to long-branch attraction, an artifact of these constraints on character states that has been well studied with molecular data (Huelsenbeck, 1997; Graybeal, 1998), but that is seldom tested with morphological data. ...
All characters and trait systems in an organism share a common evolutionary history that can be estimated using phylogenetic methods. However, differential rates of change and the evolutionary mechanisms driving those rates result in pervasive phylogenetic conflict. These drivers need to be uncovered because mismatches between evolutionary processes and phylogenetic models can lead to high confidence in incorrect hypotheses. Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species. For more than a decade, evolutionary relationships among members of the New World bat family Phyllostomidae inferred from morphological and molecular data have been in conflict. Here, we develop and apply methods to minimize systematic biases, uncover the biological mechanisms underlying phylogenetic conflict, and outline data requirements for future phylogenomic and morphological data collection. We introduce new morphological data for phyllostomids and outgroups and expand previous molecular analyses to eliminate methodological sources of phylogenetic conflict such as taxonomic sampling, sparse character sampling, or use of different algorithms to estimate the phylogeny. We also evaluate the impact of biological sources of conflict: saturation in morphological changes and molecular substitutions, and other processes that result in incongruent trees, including convergent morphological and molecular evolution. Methodological sources of incongruence play some role in generating phylogenetic conflict, and are relatively easy to eliminate by matching taxa, collecting more characters, and applying the same algorithms to optimize phylogeny. The evolutionary patterns uncovered are consistent with multiple biological sources of conflict, including saturation in morphological and molecular changes, adaptive morphological convergence among nectar-feeding lineages, and incongruent gene trees. Applying methods to account for nucleotide sequence saturation reduces, but does not completely eliminate, phylogenetic conflict. We ruled out paralogy, lateral gene transfer, and poor taxon sampling and outgroup choices among the processes leading to incongruent gene trees in phyllostomid bats. Uncovering and countering the possible effects of introgression and lineage sorting of ancestral polymorphism on gene trees will require great leaps in genomic and allelic sequencing in this species-rich mammalian family. We also found evidence for adaptive molecular evolution leading to convergence in mitochondrial proteins among nectar-feeding lineages. In conclusion, the biological processes that generate phylogenetic conflict are ubiquitous, and overcoming incongruence requires better models and more data than have been collected even in well-studied organisms such as phyllostomid bats.
... When loss of characters due to heterochronic evolution is assumed, developmental constraints must be considered additionally. Further on, selection on function and properties of developmental systems can limit the number of realized character states (Donoghue and Ree 2000), which subsequently enhance the likelihood of homoplasy. Increase of instances of convergent evolution due to the limited number of characters is well known in molecular phylogenetics (e.g. ...
Annelid relationships are controversial, and molecular and morphological analyses provide incongruent estimates. Character loss is identified as a major confounding factor for phylogenetic analyses based on morphological data. A direct approach and an indirect approach for the identification of character loss are discussed. Character loss can frequently be found within annelids and examples of the loss of typical annelid characters, like chaetae, nuchal organs, coelomic cavities and other features, are given. A loss of segmentation is suggested for Sipuncula and Echiura; both are supported as annelid ingroups in molecular phylogenetic analyses. Moreover, character loss can be caused by some modes of heterochronic evolution (paedomorphosis) and, as shown for orbiniid and arenicolid polychaetes, paedomorphic taxa might be misplaced in phylogenies derived from morphology. Different approaches for dealing with character loss in cladistic analyses are discussed. Application of asymmetrical character state transformation costs or usage of a dynamic homology framework represents promising approaches. Identifying character loss prior to a phylogenetic analysis will help to refine morphological data matrices and improve phylogenetic analyses of annelid relationships.
... Despite numerous studies of the effect of specialization on taxonomic diversification, studies of its effects on subsequent morphological diversity (disparity) are few. In a theoretical context, many workers have suggested that possession of certain morphological character states may reduce the ability to attain certain other states (Lauder 1981;Smith et al. 1985;Emerson 1988;Futuyma and Moreno 1988;Werdelin 1996;Donoghue and Ree 2000;Wagner and Schwenk 2000), implying that the subsequent evolutionary trajectories of some specialized taxa may be limited. At its extreme, therefore, specialization could act as a dead end (Moran 1988;Janz et al. 2001), limiting morphological diversification and potentially reducing rates of cladogenesis or, alternatively, increasing extinction rates as specialized taxa reduce their ability to adapt to changing conditions. ...
The effects of specialization on subsequent morphological evolution are poorly under-stood. Specialization has been implicated in both adaptive radiations that result from key inno-vations and evolutionary ''dead ends,'' where specialized characteristics appear to limit subse-quent evolutionary options. Despite much theoretical debate, however, empirical studies remain infrequent. In this paper, we use sister-group comparisons to evaluate the effect of morphological specialization to a particular ecological niche, hypercarnivory, on subsequent taxonomic and mor-phological diversity. Six sets of sister groups are identified in which one clade exhibits hypercar-nivorous characteristics and the sister clade does not. Comparison results are summed across the categories ''hypercarnivore'' and ''sister group.'' We also evaluate whether increasing degrees of specialization are correlated with decreasing phenotypic variation. Results presented here indicate that specialization to hypercarnivory has no effect on taxonomic diversity, but a strong effect on subsequent morphological diversity related to the jaws and dentition, and that increasing special-ization does not correlate with morphological diversity except in the most specialized saber-toothed taxa, which exhibit higher variance than less specialized morphs, possibly due to selection on other characteristics.
... Such morphological shifts are of special interest in relation to shifts in pollination (Neal 1998) and perhaps, ultimately, in rates of speciation (Sargent 2004). It has also been suggested that the various forms of monosymmetry found among asterids (Donoghue et al. 1998) might reflect underlying developmental constraints in this lineage, especially related to the basic orientation of the flower, that result in a medially positioned petal in the abaxial or ventral portion of the flower (Donoghue and Ree 2000). Ideas on the evolution of floral symmetry have been greatly advanced in recent years by the discovery of two potential candidate genes, CYCLOIDEA (Luo et al. 1996) and DIVARICATA (Galego and Almeida 2002). ...
Flower symmetry is of special interest in understanding the evolution and ecology of angiosperms. Evidence from the Antirrhineae (within the lamiid clade of Asteridae) indicates that several TCP gene family transcription factors, especially CYCLOIDEA (CYC), play a role in specifying dorsal identity in the corolla and androecium of monosymmetric (bilateral) flowers. We examine the evolution of this gene family in Dipsacales, representing the campanulid clade of Asteridae, in relation to evolutionary shifts in floral symmetry and stamen abortion. We identify three major forms of CYC-like genes in Dipsacales. We identify the position of additional gene duplications by comparing each of the three gene trees to a well-supported Dipsacales phylogeny. We infer duplications in two of the major gene lineages along the line leading to the Caprifoliaceae correlated with the origin of monosymmetric flowers. There are no duplications or losses associated with major shifts in stamen number. However, there are several additional duplications within the Caprifoliaceae, especially in the Morinaceae, possibly related to calyx monosymmetry and/or stamen reduction. Within the protein-coding sequences, we identify a new conserved region—the ECE region—that appears to be present across known angiosperm sequences. There are major changes in length and in the presence or absence of the ECE region in the Dipsacales, indicating changes in gene function. These studies expand our understanding of the evolution of CYC-like genes in angiosperms and provide a new system for studying the role of this gene family in determining floral form.
... Finally, these thoughts about recurrence also bear on the issue of the role of convergence vis-a `-vis the repeatability of evolution (Gould 1989; ; Conway Morris and Gould 1998). Convergences, parallelisms, and mixtures of the two surely will occur in any evolving systems, and at least for parallelisms we can make concrete predictions about the frequency of occurrence (depending on the number of branching events, the number of character states, and rates of character evolution [Donoghue and Ree 2000]). But the mere fact of recurrence, I would argue, does little to guarantee convincing repeat performances in running the tape of Life over again. ...
Improvements in our understanding of green plant phylogeny are casting new light on the connection between character evolution and diversification. The repeated discovery of paraphyly has helped disentangle what once appeared to be phylogenetically coincident character
changes, but this has also highlighted the existence of sequences of character change, no one element of which can cleanly be identified as the ‘‘key innovation’’ responsible for shifting diversification rate. In effect, the cause becomes distributed across a nested series of nodes in the tree. Many of the most conspicuous plant ‘‘innovations’’ (such as macrophyllous leaves) are underlain by earlier, more subtle shifts in development (such as overtopping growth), which appear to have enabled the exploration of a greater range of morphological designs. Often it appears that these underlying changes have been brought about at the level of cell interactions within meristems, highlighting the need for developmental models and experiments focused at this level. The standard practice of attempting to identify correlations between recurrent character change (such as the tree growth habit) and clade diversity is complicated by the observation that the ‘‘same’’ trait may be constructed quite differently in different lineages (e.g., different forms of cambial activity), with some solutions imposing more architectural limitations than others. These thoughts highlight the need for a more nuanced view, which has implications for comparativemethods. They also bear on issues central to Stephen Jay Gould’s vision of macroevolution, including exaptation and evolutionary recurrence in relation to constraint and the repeatability of evolution.
... A critical fi rst step toward a synthesis of evolution, development, and function is therefore the identifi cation and evolutionary analysis of such repeatedly evolving character cohorts ( Jabbour et al., 2008 ). The use of molecular phylogenetic data are essential in this regard because they provide an independent framework for the reconstruction of ancestral states, making possible the explicit dissection and quantifi cation of structural homoplasy ( Donoghue and Sanderson, 1994 ;Donoghue and Ree, 2000 ). Furthermore, they permit the use of comparative methods to test correlated transitions between two characters in evolution ( Givnish et al., 2005 ). ...
The unique properties of tree building in Arecaceae strongly constrain their architectural lability. Potentially compensating for this limitation, the extensive diversification of leaf anatomical structure within palms involves many characters whose alternate states may confer disparate mechanical or physiological capabilities. In the context of a recent global palm phylogeny, we analyzed the evolution of 10 such lamina anatomical characters and leaf morphology of 161 genera, conducting parsimony and maximum likelihood ancestral state reconstructions, as well as tests of correlated evolution. Lamina morphology evolves independently from anatomy. Although many characters do optimize as synapomorphic for major clades, anatomical evolution is highly homoplasious. Nevertheless, it is not random: analyses indicate the recurrent evolution of different cohorts of correlated character states. Notable are two surface layer (epidermis and hypodermis) types: (1) a parallel-laminated type of rectangular epidermal cells with sinuous anticlinal walls, with fibers present in the hypodermis and (2) a cross-laminated type of hexagonal cells in both layers. Correlated with the cross-laminated type is a remarkable decrease in the volume fraction of fibers, accompanied by changes in the architecture and sheath cell type of the transverse veins. We discuss these and other major patterns of anatomical evolution in relation to their biomechanical and ecophysiological significance.
... An additional factor that affects morphospace evolution is homoplasy, the tendency of characters to attain recurrent states by reversal, convergent, or parallel evolution. Even under frequent character changes, a lineage will fail to explore fundamentally new regions of morphospace if these changes represent reversals to ancestral conditions or parallellisms with other lineages (31,32). Although homoplastic changes may increase tadpole diversity by generating new combinations of character states, the dimensionality of morphospace (and thus, the level of disparity among taxa) will remain limited without the exploration of new states. ...
Anurans (frogs and toads) are unique among land vertebrates in possessing a free-living larval stage that, parallel to adult frogs, diversified into an impressive range of ecomorphs. The tempo and mode at which tadpole morphology evolved through anuran history as well as its relationship to lineage diversification remain elusive. We used a molecular phylogenetic framework to examine patterns of morphological evolution in tadpoles in light of observed episodes of accelerated lineage diversification. Our reconstructions show that the expansion of tadpole morphospace during the basal anuran radiation in the Triassic/Early Jurassic was unparalleled by the basal neobatrachian radiation in the Late Jurassic/Early Cretaceous or any subsequent radiation in the Late Cretaceous/Early Tertiary. Comparative analyses of radiation episodes indicate that the slowdown of morphospace expansion was caused not only by a drop in evolutionary rate after the basal anuran radiation but also by an overall increase in homoplasy in the characters that did evolve during later radiations. The overlapping sets of evolving characters among more recent radiations may have enhanced tadpole diversity by creating unique combinations of homoplastic traits, but the lack of innovative character changes prevented the exploration of fundamental regions in morphospace. These complex patterns transcend the four traditionally recognized tadpole morphotypes and apply to most tissue types and body parts.
... network structure. For example, the fascinating enigma of plant evolutionary novelties such as leaf morphogenesis [69], the development of drought resistance [70] and the establishment of floral symmetry [71] might be solved. ...
Recent evolutionary studies clearly indicate that evolution is mainly driven by changes in the complex mechanisms of gene regulation and not solely by polymorphism in protein-encoding genes themselves. After a short description of the cis-regulatory mechanism, we intend in this review to argue that by applying newly available technologies and by merging research areas such as evolutionary and developmental biology, population genetics, ecology and molecular cell biology it is now possible to study evolution in an integrative way. We contend that, by analysing the effects of promoter sequence variation on phenotypic diversity in natural populations, we will soon be able to break the barrier between the study of extant genetic variability and the study of major developmental changes. This will lead to an integrative view of evolution at different scales. Because of their sessile nature and their continuous development, plants must permanently regulate their gene expression to react to their environment, and can, therefore, be considered as a remarkable model for these types of studies.
... Although experiments may reproduce ancestral phenotypes, alternative developmental pathways may exist. Exploring the potential range of phenotypes [evolvable states (15)] to reveal genetic mechanisms involved with macroevolutionary processes is likely to be fruitful. ...
Understanding the diversification of phenotypes through time—“descent with modification”—has been the focus of evolutionary
biology for 150 years. If, contrary to expectations, similarity evolves in unrelated taxa, researchers are guided to uncover
the genetic and developmental mechanisms responsible. Similar phenotypes may be retained from common ancestry (homology),
but a phylogenetic context may instead reveal that they are independently derived, due to convergence or parallel evolution,
or less likely, that they experienced reversal. Such examples of homoplasy present opportunities to discover the foundations
of morphological traits. A common underlying mechanism may exist, and components may have been redeployed in a way that produces
the “same” phenotype. New, robust phylogenetic hypotheses and molecular, genomic, and developmental techniques enable integrated
exploration of the mechanisms by which similarity arises.
There are few cases where numbers or types of possible phenotypes are known, although vast state spaces have been postulated. Rarely applied in this context, graph theory and topology enable enumeration of possible phenotypes and evolutionary transitions. Here, we generate polyhedral calyx graphs for the Late Cretaceous, stemless crinoids Marsupites testudinarius and Uintacrinus socialis (Uintacrinoidea Zittel) revealing structural similarities to carbon fullerene and fulleroid molecules (respectively). The U. socialis calyx incorporates numerous plates (e.g. graph vertices |V| ≥ 197), which are small, light, low‐density and have four to eight sides. Therefore, the corresponding number of possible plate arrangements (number of polyhedral graphs) is large (≫1 × 1014). Graph vertices representing plates with sides >6 introduce negative Gaussian curvature (surface saddle points) and topological instability, increasing buckling risk. However, observed numbers of vertices for Uintacrinus do not allow more stable pentaradial configurations. In contrast, the Marsupites calyx dual graph has 17 faces that are pentagonal or hexagonal. Therefore, it is structurally identical to a carbon fullerene, specifically C30‐D5h. Corresponding graph restrictions result in constraint to only three structural options (fullerene structures C30‐C2v 1, C30‐C2v 2 and C30‐D5h). Further restriction to pentaradial symmetry allows only one possibility: the Marsupites phenotype. This robust, stable topology is consistent with adaptation to predation pressures of the Mesozoic marine revolution. Consequently, the most plausible evolutionary pathway between unitacrinoid phenotypes was a mixed heterochronic trade‐off to fewer, larger calyx plates. Therefore, topological limitations radically constrained uintacrinoid skeletal possibilities but thereby aided evolution of a novel adaptive phenotype.
The phylogenetic placement of the Old World Gesneriaceae genera Ramonda, Conandron, Bournea, Thamnocharis, and Tengia, all characterized by actinomorphic flowers, has been the subject of much debate. Actinomorphy in Gesneriaceae is rare, with most species exhibiting zygomorphic flowers. The actinomorphic genera have historically been considered “primitive” and lumped in the tribe Ramondeae separate from the remaining Old World Gesneriaceae. In this study, we used nuclear (ITS) and plastid (trnL‐F) DNA for molecular phylogenetic analysis of these five genera along with representative species across the Cyrtandroideae. Our results show that the actinomorphic genera are scattered over several otherwise zygomorphic clades within Cyrtandroideae, and along with previous data, indicate that Ramondeae is an unnatural group. Floral actinomorphy has evolved convergently in different alliances of Old World Gesneriaceae. Ramonda is sister to Haberlea, Bournea is apparently paraphyletic, Conandron seems rather isolated, and Tengia is close to Petrocodon and sister to a group of Chirita sect. Gibbosaccus together with Calcareoboea. We hypothesize that the evolution from zygomorphy to actinomorphy with novel combinations of characters is possibly due to shifts in pollination strategies, such as a switch from nectar‐ to pollen‐rewards.
Abiotic filters have been found either to increase or reduce evolutionary relatedness in plant communities, making it difficult to generalize responses of this major feature of biodiversity to future environmental change. Here, we hypothesized that the responses of phylogenetic structure to environmental change ultimately depend on how species have evolved traits for tolerating the resulting abiotic changes.
Working within ephemeral wetlands, we tested whether species were increasingly related as flooding duration intensified. We also identified the mechanisms underlying increased relatedness by measuring root aerenchyma volume ( RAV ), a trait which promotes waterlogging tolerance.
We found that species‐specific responses to flooding explained most of the variation in occurrence for 63 vascular plant species across 5170 plots. For a subset of 22 species, we attributed these responses to variation in RAV . Large RAV specifically increased occurrence when flooding lasted for longer time periods, because large RAV reduced above‐ground biomass loss. As large RAV was evolutionarily conserved within obligate wetland species, communities were more phylogenetically related as flooding increased.
Our study shows how reconstructing the evolutionary history of traits that influence the responses of species to environmental change can help to predict future patterns in phylogenetic structure.
Introduction
To understand the role of adaptation in generating macroevolutionary patterns, it is necessary to understand whether and in what ways specific features of the phenotype affect subsequent phenotypic diversification. This area has been much debated by both past and present workers, some of who considered whether certain morphologies might be ‘channelled’ (e.g. Gould, 1984; Emerson, 1988; Wagner, 1996) to appear once a specific starting morphology was attained. Less radically, a number of workers have suggested that possession of certain morphological character states may reduce the ability to attain certain other character states (Lauder, 1981; Maynard-Smith et al., 1985; Emerson, 1988; Futuyma and Moreno, 1988; Wagner, 1996; Werdelin, 1996; Alroy, 2000; Donoghue and Ree, 2000; Wagner and Schwenk, 2000; Wagner, 2001; Wagner and Mueller, 2002; Porter and Crandal, 2003; Van Valkenburgh et al., 2004; Polly, 2008), implying that, in some cases, taxa may be limited in their subsequent evolutionary trajectories. Both morphological channelling and a limitation on specific character states fall into the realm of a character change bias, where certain states are more likely to appear than others (Sanderson, 1993; Wagner, 1996; Donoghue and Ree, 2000; Wagner, 2001; Goldberg and Igic, 2008; Polly, 2008). Despite ongoing theoretical debate, however, there has been relatively little empirical exploration of the possibility of bias or directionality in morphological character change, and this area remains poorly understood (Arthur, 2001, 2004; Schluter et al., 2004).
An enduring puzzle in evolutionary biology is to understand how individuals and populations adapt to fluctuating environments. Here we present an integro-differential model of adaptive dynamics in a phenotype-structured population whose fitness landscape evolves in time due to periodic environmental oscillations. The analytical tractability of our model allows for a systematic investigation of the relative contributions of heritable variations in gene expression, environmental changes and natural selection as drivers of phenotypic adaptation. We show that environmental fluctuations can induce the population to enter an unstable and fluctuation-driven epigenetic state. We demonstrate that this can trigger the emergence of oscillations in the size of the population, and we establish a full characterisation of such oscillations. Moreover, the results of our analyses provide a formal basis for the claim that higher rates of epimutations can bring about higher levels of intrapopulation heterogeneity, whilst intense selection pressures can deplete variation in the phenotypic pool of asexual populations. Finally, our work illustrates how the dynamics of the population size is led by a strong synergism between the rate of phenotypic variation and the frequency of environmental oscillations, and identifies possible ecological conditions that promote the maximisation of the population size in fluctuating environments.
Phylogenetic studies of lineages growing in extreme environments have frequently recovered evidence not only of high level of homoplasy but also of discordance of morphological disparity and species diversity. It has been suggested that this divergence may be caused by developmental constraints and/or natural selection. Here we explored these hypotheses by inferring the phenotypic evolution of the derived liverwort genus Cololejeunea. These liverworts occur preferentially on the surface of leaves or other aerial parts of vascular plants growing in wet forests. The evolution of 12 morphological characters was studied using a phylogenetic framework comprising 70 species of Cololejeunea. The phylogeny was reconstructed using DNA sequences of one nuclear and two plastid regions and enabled the inference of the evolution of the studied morphological characters by determining the frequency of homoplasy. Mantel tests were used to test for correlations of morphological disparity × species diversity and morphological disparity × epiphytism. The phylogenetic informativeness of each binary character was estimated by the D metric of the Fritz and Purvis test, and the relationship between each character and epiphytism was inferred by Pearson’s coefficient. We evaluated the morphospace occupation using principal coordinate analyses. Our results not only recovered high levels of homoplasy but also weak correlations of morphological disparity and species diversity. Morphological disparity was not linked to epiphytism, although positive or negative relationships between some characters and epiphytism were found. The Brownian model of character evolution was not rejected for the studied morpho- logical disparity in Cololejeunea with the exception of asexual propagules. The observations support the prediction that iterative evolution in a well-defined morphospace may result in rampant homoplasy and the observed divergence of disparity and diversity.
Evidence from Antirrhinum majus indicates that transcription factors CYCLOIDEA (CYC), DIVARICATA (DIV), and RADIALIS (RAD) play a role in specifying floral symmetry. In bilaterally symmetrical flowers, CYC and RAD are implicated in dorsal identity, while DIV patterns ventral identity. In this study, we examined duplication events within the RAD-like gene family in Dipsacales and report the phylogenetic relationships of the RAD-like genes across Pentapetaleae. Like CYC-like and DIV-like genes, we found three Pentapetaleae clades of RAD-like genes: RAD1, RAD2, and RAD3, with AmRAD in the RAD2 clade. Unlike CYC-like and DIV-like gene families, only one of these duplications appears to have taken place around the diversification of the Pentapetaleae: RAD1 spans the monocots and eudicots, while RAD2 and RAD3 are Pentapetaleae specific. We found additional duplications within these gene clades in Dipsacales, especially within the Morinaceae, Dipsacaceae, and Valerianaceae, which also contain additional duplications in CYC-like and DIV-like genes. Using reverse transcription polymerase chain reaction, we show that most RAD copies are expressed across floral and leaf tissues in Lonicera × bella. DipsRAD2B (orthologous to AmRAD) is expressed in a dorsoventral pattern similar to DipsCYC2B, which is similar to the result in A. majus. We argue that this favors the hypothesis that a similar interaction between CYC and RAD may occur outside of the Lamiales.
Since its inception in the early 1980s, evo-devo has evolved into a mature discipline. This is manifest in the naming of research groups, scientific journals and books, pr Of essional meetings and societies. Despite such formal attributes of a scientific discipline it is often unclear what constitutes its conceptual distinctiveness. Does evo-devo have its own set of specific questions and research methods? Does it solve biological problems that cannot be solved by other approaches? And does it represent a significant change in the theoretical understanding of development and evolution? That is, in which way do the goals, the empirical programs and the theories of evo-devo research differ from those of neighbouring disciplines such as developmental biology or evolutionary biology? The present chapter provides a concise overview of the current status of evo-devo as a discipline. This requires a short reflection on its history. CONCEPTUAL FOUNDATIONS The parallels between embryonic stages and the ‘scale of beings’ had already been contemplated in pre-Darwinian times, and the foundation of a scientific theory of evolution was significantly influenced by embryological arguments. Darwin called embryology ‘by far the strongest single class of facts in favour of a change of form’, and his first sketches of a phylogenetic tree seem to have been inspired by tree-like renderings of embryological differences between species (Richards 1992). Much of the early work in evolutionary biology focused on the uses of embryonic characters for taxonomical purposes. © Cambridge University Press 2008 and Cambridge University Press, 2009.
Transferability and application of microsatellites (SSRs) from Juniperus communis L. to Juniperus procera Hochst. Ex endl. ABSTRACT Transferability of five nuclear microsatellite markers (Jc-16, Jc-31, Jc-32, Jc-35 and Jc-37) that were origi-nally developed for J. communis was tested to J. pro-cera. Jc-31 & Jc-37 showed successful amplifications and polymorphism in J. procera. Jc-35 which had been reported as polymorphic in J. communis was monomorphic in J. procera while the primer pair for Jc-32 failed to record any amplification. The remain-ing one primer pair (Jc-16) showed double loci ampli-fication in both J. procera and the control J. commu-nis suggesting further examination of the primer pair and its binding sites. Genetic variation of six Ethio-pian J. procera populations: Chilimo, Goba, Mena-gesha-Suba, Wef-Washa, Yabelo and Ziquala was as-sessed based on the two polymorphic loci (Jc-31 & Jc-37) in 20 -24 individuals of each population. From these two loci, a total of 41 alleles could be retrieved. Two populations that are located south east of the Great Rift Valley together harboured 75% of private alleles signifying their deviant geo-ecological zones and suggesting special consideration for conservation. Chilimo, which is at the western margin of Juniper habitat in Ethiopian central highlands scored the highest fixation (F IS = 0.584) entailing lower immi-grant genes and hence higher inbreeding. The AMOVA revealed that 97% of the variation resided within the populations while still among population variation was significant (p < 0.05).
The phylogenetic placement of the Old World Gesneriaceae genera Ramonda, Conandron, Bournea, Thamnocharis, and Tengia, all characterized by actinomorphic flowers, has been the subject of much debate. Actinomorphy in Gesneriaceae is rare, with most species exhibiting zygomorphic flowers. The actinomorphic genera have historically been considered “primitive and lumped in the tribe Ramondeae separate from the remaining Old World Gesneriaceae. In this study, we used nuclear (ITS) and plastid (trnL-F) DNA for molecular phylogenetic analysis of these five genera along with representative species across the Cyrtandroideae. Our results show that the actinomorphic genera are scattered over several otherwise zygomorphic clades within Cyrtandroideae, and along with previous data, indicate that Ramondeae is an unnatural group. Floral actinomorphy has evolved convergently in different alliances of Old World Gesneriaceae. Ramonda is sister to Haberlea, Bournea is apparently paraphyletic, Conandron seems rather isolated, and Tengia is close to Petrocodon and sister to a group of Chirita sect. Gibbosaccus together with Calcareoboea. We hypothesize that the evolution from zygomorphy to actinomorphy with novel combinations of characters is possibly due to shifts in pollination strategies, such as a switch from nectar- to pollen-rewards.
Using a morphological dataset of 136 vegetative and reproductive characters, we infer the tracheophyte phylogeny with an emphasis on early divergences of ferns (monilophytes). The dataset comprises morphological, anatomical, biochemical, and some DNA structural characters for a taxon sample of 35 species, including representatives of all major lineages of vascular plants, especially ferns. Phylogenetic relationships among vascular plants are reconstructed using maximum parsimony and Bayesian inference. Both approaches yield similar relationships and provide evidence for three major lineages of extant vascular plants: lycophytes, ferns, and seed plants. Lycophytes are sister to the euphyllophyte clade, which comprises the fern and seed plant lineages. The fern lineage consists of five clades: horsetails, whisk ferns, ophioglossoids, marattioids, and leptosporangiate ferns. This lineage is supported by characters of the spore wall and has a parsimony bootstrap value of 76%, although the Bayesian posterior probability is only 0.53. Each of the five fern clades is well supported, but the relationships among them lack statistical support. Our independent phylogenetic analyses of morphological evidence recover the same deep phylogenetic relationships among tracheophytes as found in previous studies utilizing DNA sequence data, but differ in some ways within seed plants and within ferns. We discuss the extensive independent evolution of the five extant fern clades and the evidence for the placement of whisk ferns and horsetails in our morphological analyses.
Key Words community assembly and organization, phylogenetic conservatism, biogeography, species diversity, niche differentiation s Abstract As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evo-lutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phy-logenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emer-gent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, charac-ter reconstruction, null models for community assembly and character evolution, and metrics of community phylogenetic structure underlie the recent progress in these ar-eas. We highlight the potential for community ecologists to benefit from phylogenetic knowledge and suggest several avenues for future research.
Distinguishing convergent evolution from other causes of similarity in organisms is necessary for reconstructing phylogenetic relationships, inferring patterns of character evolution, and investigating the forces of natural selection. In contrast to animals and land plants, the pervasiveness and adaptive significance of convergent evolution in microbes has yet to be systematically explored or articulated. Convergent evolution in microbial eukaryotes, for instance, often involves very distantly related lineages with relatively limited repertoires of morphological features. These large phylogenetic distances weaken the role of ancestral developmental programs on the subsequent evolution of morphological characters, making convergent evolution between very distantly related lineages fundamentally different from convergent evolution between closely related lineages. This suggests that examples of convergence at different levels in the phylogenetic hierarchy offer different clues about the causes and processes of macroevolutionary diversification. Accordingly (and despite opinions to the contrary), I recognize three broad and overlapping categories of phenotypic convergence—“parallel”, “proximate” and “ultimate”—that represent either (1) subcellular analogues, (2) subcellular analogues to multicellular systems (and vice versa), or (3) multicellular analogues. Microbial eukaryotes living in planktonic environments, interstitial environments, and the intestinal environments of metazoan hosts provide compelling examples of ultimate convergence. After describing selected examples in microbial eukaryotes, I suggest some future directions needed to more fully understand the hierarchical structure of convergent evolution and the overall history of life.
Evolutionary diversification of a phenotypic trait reflects the tempo and mode of trait evolution, as well as the phylogenetic topology and branch lengths. Comparisons of trait variance between sister groups provide a powerful approach to test for differences in rates of diversification, controlling for differences in clade age. We used simulation analyses under constant rate Brownian motion to develop phylogenetically based F-tests of the ratio of trait variances between sister groups. Random phylogenies were used for a generalized evolutionary null model, so that detailed internal phylogenies are not required, and both gradual and speciational models of evolution were considered. In general, phylogenetically structured tests were more conservative than corresponding parametric statistics (i.e., larger variance ratios are required to achieve significance). The only exception was for comparisons under a speciational evolutionary model when the group with higher variance has very low sample size (number of species). The methods were applied to a large data set on seed size for 1976 species of California flowering plants. Seven of 37 sister-group comparisons were significant for the phylogenetically structured tests (compared to 12 of 37 for the parametric F-test). Groups with higher diversification of seed size generally had a greater diversity of fruit types, life form, or life history as well. The F-test for trait variances provides a simple, phylogenetically structured approach to test for differences in rates of phenotypic diversification and could also provide a valuable tool in the study of adaptive radiations.
The island of Madagascar ranks second to the neotropics in diversity of Bignoniaceae. Tribe Coleeae (Bignoniaceae) is a monophyletic
group of tropical trees endemic to Madagascar and surrounding islands. The Masoala assemblage of Coleeae, in northeastern
Madagascar, utilizes four mechanisms for avoiding competition via niche specialization: (1) morphologically via characters
that comprise syndromes, explaining part of the pattern in this system – although the syndrome concept is not perfect; (2)
spatially via vertical stratification and potentially pollen placement; (3) temporally via phenological stagger; (4) ethologically
via flowering duration and display. The 13 sympatric species of understory treelets and canopy trees did receive low flower visitor numbers. Contrary to the prevailing view of pollination systems where generalized systems predict
equivalency between floral traits and pollinators, I found that different pollinators pollinated the 13 species of trees, that floral characters of different trees did not overlap in multidimensional phenotype space, and that few species of trees were visited by more than two pollinator groups. The use of multiple niches is potentially important in
understanding both the origin and maintenance of tropical tree diversity.
The cacti have undergone extensive specialization in their evolutionary history, providing an excellent system in which to address large-scale questions of morphological and physiological adaptation. Recent molecular phylogenetic studies suggest that (1) Pereskia, the leafy genus long interpreted as the sister group of all other cacti, is likely paraphyletic, and (2) Cactaceae are nested within a paraphyletic Portulacaceae as a member of the "ACPT" clade (Anacampseroteae, Cactaceae, Portulaca, and Talinum). We collected new data on the vegetative anatomy of the ACPT clade and relatives to evaluate whether patterns in the distributions of traits may provide insight into early events in the evolutionary transition to the cactus life form. Many traits had high levels of homoplasy and were mostly equivocal with regard to infraclade relationships of ACPT, although several characters do lend further support to a paraphyletic Pereskia. These include a thick stem cuticle, prominent stem mucilage cells, and hypodermal calcium oxalate druses, all of which are likely to be important traits for stem water storage and photosynthesis. We hypothesize that high lability of many putative "precursor" traits may have been critical in generating the organismal context necessary for the evolution of an efficient and integrated photosynthetic stem.
One of the advantages frequently cited for the use of DNA sequence data in phylogeny reconstruction is that explicit models of character evolution, based on our understanding of sequence evolution, may be incorporated into the analysis. In this way the method for recovering the pattern of evolutionary divergence can be tied more closely to the processes that produce the variation (Clegg and Zurawski, 1992; Simon et al., 1994; Moritz and Hillis, 1996). Within the context of parsimony analysis, it has been assumed that the reliability of information for phylogeny reconstruction can be inferred from estimates of substitution rate for different sites, with the most slowly evolving sites being the most reliable and, therefore, most heavily weighted (Farris, 1969, 1977; Felsenstein 1981a; Swofford et al. 1996). However, parsimony analyses based on chloroplast DNA (cpDNA) typically are conducted with equal weight given to all changes (e.g., Kim et al., 1992; Olmstead et al., 1993; Price and Palmer, 1993; Hoot et al., 1995; Johnson and Soltis, 1995; Gadek et al., 1996). The main reasons for this may be historical, stemming from a reluctance to weight characters in morphological cladistic analyses, or operational, due to the difficulty of implementing the more complicated analyses necessary for incorporating weights in phylogenetic analysis. In addition, there is a paucity of statistical analyses of cpDNA sequence substitution patterns (Clegg, 1993), which results in an inability to provide a firm basis for establishing weights.
A diverse array of molecular approaches is now available to the plant systematist for use in phylogenetic inference, including restriction site analysis, comparative sequencing, analysis of DNA rearrangements (e.g., inversions) and gene and intron loss, and various PCR-based techniques. Although these various methodologies present systematists with unparalleled opportunities for elucidating relationships and evolutionary processes, the sheer number of molecular approaches available, as well as the number of proven DNA regions for use in comparative sequencing, may seem overwhelming to those new to the field of molecular systematics. This chapter provides a general review of the various molecular techniques currently available to the plant systematist. Our primary goal is to review the types of molecular data sets that can presently be obtained; we discuss the advantages and disadvantages of each and the most appropriate approach for studying a given taxonomic level or type of evolutionary question. Given the current emphasis on DNA sequence data for phylogeny estimation, we then concentrate on the choice of an appropriate gene for comparative sequencing and also briefly discuss the pros and cons of manual versus automated sequencing. A description of selected PCR- mediated techniques for systematic and population-level studies is presented in Chapter 2.
In the quantitative phyletic approach to evolutionary taxonomy, quantitative methods are used for inferring evolutionary relationships. The methods are chosen both for their operationism and for their connection to evolutionary theory and the goals of evolutionary taxonomy. As an example of this approach, a detailed analysis of a set of anuran characters is presented and taxonomic conclusions based on those characters are drawn. The methods and conclusions of the quantitative phyletic analysis are compared and contrasted with the methods of previous workers in the field of anuran classification.
The internal transcribed spacer (ITS) region of 18S-26S nuclear ribosomal DNA (nrDNA) has proven to be a useful source of characters for phylogenetic studies in many angiosperm families. The two spacers of this region, ITS-1 and ITS-2 (each <300 bp), can be readily amplified by PCR and sequenced using universal primers, even from DNAs of herbarium specimens. Despite high copy numbers of both spacers, the near uniformity of ITS paralogues, attributed to rapid concerted evolution, allows direct sequencing of pooled PCR products in many species. Divergent paralogues, where detected, require cloning, but may offer a means of obtaining multiple estimates of organismal relationships and of determining placement of the root in a phylogeny independent of outgroup considerations. In reported studies, variation between ITS sequences is mostly attributable to point mutations. A relatively minor proportion of sites is affected by insertions or deletions (indels) among sequences that are similar enough to have retained sufficient signal for phylogenetic analysis. Within these limits, sequence alignment is generally unambiguous except in small regions of apparently lower structural constraint. Phylogenetic analyses of combined data sets from both spacers, where examined, yield trees with greater resolution and internal support than analyses based on either spacer alone. This beneficial effect of simultaneous analysis is not surprising based on the low number of useful characters in each spacer. This effect also suggests high complementarity of spacer data, in accord with similarity in size, sequence variability, and G + C content of ITS-1 and ITS-2 in most investigated groups of closely related angiosperms. Nonindependent evolution of ITS sites involved in intraspacer RNA base-pairing may occur, given possible functional constraints, but preliminary secondary structure analyses of ITS-2 in Calycadenia (Asteraceae) show no definite evidence of compensatory spacer mutations. As expected, levels of ITS sequence variation suitable for phylogenetic analysis are found at various taxonomic levels within families, depending on the lineage. The apparent rates of ITS molecular evolution are roughly correlated with plant life-form, as with chloroplast DNA (cpDNA) data, but reasons for this observation are unclear. ITS characters have improved our understanding of angiosperm phylogeny in several groups by (1) corroborating earlier unexpected findings, (2) resolving conflicts between other data sets, (3) improving resolution of species relationships, or (4) providing direct evidence of reticulate evolution. Hybridization or sorting of ancestral polymorphism in a lineage can complicate interpretation of trees based on any type of evolutionary evidence, including ITS or cpDNA sequences, particularly in the absence of at least one independent phylogenetic data set from the same organisms. The need for phylogenetic markers from the nuclear genome, to complement the rapidly growing body of cpDNA data, makes the ITS region a particularly valuable resource for plant systematists.
•In an attempt to clarify the relevance of ontogenetic transformations for system- atics, the ontogenetic method for determining character polarity (the biogenetic law of Nelson, 1978) is analyzed from the perspective of phylogenetic systematics. In phylogenetic systematics, as defined here, the relationships sought are those of common ancestry and, thus, the concept of phylogeny is taken as an axiom from which systematic methods are deduced. This perspective has a number of consequences concerning the role of ontogenetic transformations in system-
Similarity in morphological form may arise from common ancestry (failure to evolve), from parallel evolution, from convergence, or from reversal to an apparently ancestral condition. Homoplasy from convergence, parallelism, and reversal is common, and its ubiquity creates difficulties in phylogenetic analysis. Convergent evolution often is considered one of the most powerful lines of evidence for adaptive evolution. But an alternative explanation for convergence and other evolved similarities is that limited developmental and structural options exist. Identical forms can be obtained when particular developmental phenomena are triggered by very different kinds of stimuli or when constraints exist that shape external form or limit morphological expression to a few options. Examples from plethodontid salamanders are used to illustrate an approach combining internalist and externalist analytical methods. In order to explain how morphologies evolve in lineages, both functionalist and structuralist approaches are necessary, combined in a context in which phylogenetic hypotheses and their tests are continuously pursued. When homoplasy is rampant, as in salamanders, we can expect discordance with phylogenetic analyses based on nonmorphological data sets.
Hypothesized relationships between ontogenetic and phylogenetic change in morphological characters were empirically tested in centrarchid fishes by comparing observed patterns of character development with patterns of character evolution as inferred from a representative phylogenetic hypothesis. This phylogeny was based on 56–61 morphological characters that were polarized by outgroup comparison. Through these comparisons, evolutionary changes in character ontogeny were categorized in one of eight classes (terminal addition, terminal deletion, terminal substitution, non-terminal addition, non-terminal deletion, non-terminal substitution, ontogenetic reversal and substitution). The relative frequencies of each of these classes provided an empirical basis from which assumptions underlying hypothesized relationships between ontogeny and phylogeny were tested. In order to test hypothesized relationships between ontogeny and phylogeny that involve assumptions about the relative frequencies of terminal change (e.g. the use of ontogeny as a homology criterion), two additional phylogenies were generated in which terminal addition and terminal deletion were maximized and minimized for all characters. Character state change interpreted from these phylogenies thus represents the maxima and minima of the frequency range of terminal addition and terminal deletion for the 8.7 × 10³⁶ trees possible for centrarchids.
Developmental constraints (defined as biases on the production of variant phenotypes or limitations on phenotypic variability caused by the structure, character, composition, or dynamics of the developmental system) undoubtedly play a significant role in evolution. Yet there is little agreement on their importance as compared with selection, drift, and other such factors in shaping evolutionary history. This review distinguishes between "universal" and "local" constraints; it deals primarily with the latter, which apply to a limited range of taxa. Such constraints, typically, can be broken even within the taxa to which they apply, though with varying degrees of difficulty. The origin of constraints is discussed, five distinctive of constraint being explicitly considered. Three means of identifying constraints are set forth, as well as four means of distinguishing developmental from selective constraints. None of the latter (use of a priori adaptive predictions, direct measurement of selection, direct meas...
Phylogenetic analysis of DNA sequences of the chloroplast genes rcbL and ndhf revealed a highly supported clade composed of the families Plantaginaceae, Callitrichaceae, and Hippuridaceae in close association with the model organism Antirrhinum majus and other members of family Scrophulariaceae. Plantago has miniature actinomorphic wind-pollinated flowers that have evolved from zygomorphic animal-pollinated precursors. The aquatic Hippuridaceae have reduced windpollinated flowers with one reproductive organ per whorl, and three, rather than four, whorls. In monoecious aquatic Callitrichaceae, further reduction has occurred such that there is only one whorl per flower containing a single stamen or carpel. Optimization of character states showed that these families descended from an ancestor similar to Antirrhinum majus. Recent studies of plant developmental genetics have focused on distantly related species. Differences in the molecular mechanisms controlling floral development between model organisms are difficult to interpret due to phylogenetic distance. In order to understand evolutionary changes in floral morphology in terms of their underlying genetic processes, closely related species exhibiting morphological Variation should be examined. Studies of genes that regulate morphogenesis in the clade described here could aid in the elucidation of a general model tot such fundamental issues as how changes in floral symmetry, organ number, and whorl number are achieved, as well as providing insight on the evolution of dicliny and associated changes in pollination syndrome.
Nelson, G. (Department of Ichthyology, The American Museum of Natural History, New York, New York 10024) 1978. Ontogeny, Phylogeny,
Paleontology, and the Biogenetic Law. Syst. Zool. 27:324–345.—The biogenetic law is restated in a falsifiable form: given an onto-genetic character transformation, from a character observed
to be more general to a character observed to be less general, the more general character is primitive and the less general
advanced. The law, as restated, may be generally valid. In any case, the ontogenetic argument is a valid direct technique
of character phylogeny; the anatomical argument (“outgroup comparison”) is an indirect technique; the paleontological argument
is of uncertain status. Falsification of all three types of arguments is explored in an analysis of L. Agassiz's concept of
“threefold parallelism.” Neoteny is a falsifier not of the biogenetic law, but of character phylogeny-of all three arguments.
Phylogenetic reconstruction in its entirety appears to be an extrapolation of the orderliness of development.
A method for quantifying levels of observed homoplasy in cladistic analyses is proposed. The homoplasy slope is a function
that describes the relationship between number of taxa in a cladistic analysis and the observed number of extra steps per
character. The homoplasy slope ratio (HSR) relates the homoplasy slope of a cladistic analysis (real data) to that of an analysis
based on random binary data sets of the same size. Tests show that HSR is not correlated with numbers of characters and taxa,
and this quality makes the index particularly useful for comparing the levels of observed homoplasy among cladistic analyses
based on data sets of different sizes. All of the other homoplasy indices currently available including the consistency index
(CI), retention index (RI), and homoplasy excess ratio (HER) are correlated with number of characters and or number of taxa.
Molecular genetic studies in Arabidopsis thaliana and other higher-eudicot flowering plants have led to the development of the 'ABC' model of the determination of organ identity in flowers, in which three classes of gene, A, B and C, are thought to work together to determine organ identity. According to this model, the B-class genes APETALA3 (AP3) and PISTILLATA (PI) act to specify petal and stamen identity. Here we test whether the roles of these genes are conserved throughout the angiosperms by analysing the expression of AP3 and PI orthologues in the lower eudicot subclass Ranunculidae. We show that, although expression of these orthologues in the stamens is conserved, the expression patterns in the petals differ from those found in the higher eudicots. The differences between these expression patterns suggest that the function of AP3 and PI homologues as B-class organ-identity genes is not rigidly conserved among all angiosperms. These observations have important implications for understanding the evolution of both angiosperm petals and the genetic mechanisms that control the identities of floral organs.
Studies of ontogenetic processes are fundamentally dependent on hypotheses of phylogeny. The model of Alberch et al. (1979) is reformulated in terms of phylogenetics and used to describe how heterochronic ontogenetic processes can be detected in nature. Heterochronic processes producing paedomorphosis can result in morphologies which resemble primitive (retained ancestral) traits; the conditions under which paedomorphic and primitive features can and cannot be distinguished are described. The utility of ontogeny for determination of evolutionary character transformations and character polarity and for detection of convergence and parallelism are considered. The ontogenetic criterion for assessing polarity is independent of hypotheses of phylogeny and may be as effective as outgroup comparison. Ontogenetic analysis may aid in the detection of convergence but not in the detection of parallelism.
Renewed interest in phylogenies over the last few decades coincides with a growing sense that it will actually be possible to obtain an accurate picture of evolutionary history. Indeed, the prospects of retrieving phylogeny now seem better than ever, owing to basic theoretical advance (due mainly to Hennig, 1966), the availability of computer programs that can handle large data sets, and the accessibility of new sources of evidence, especially molecular characters.
The innate-acquired distinction has long been a point of connection between evolutionary questions and developmental questions. It is also one of our oldest conceptual tools, dating back at least to the time of Plato. Further, it hs been broadly applied not just in development biology, animal ethology, and evolutionary theory, but also in epistemology, metaphysics, ethics, philosophy of science, cognitive psychology, linguistics, neurophysiology and in theories about the nature and evolution of human sociality, culture, and morality. As befits any concept which has cast such a broad and deep shadow, it has at some times and places been highly honored and at others most deeply dishonored. It has been viewed as an agent of progress and of stagnation, of clarity and of confusion, and of liberation and of bondage.
This chapter explores various senses of complexity and develops a scheme for organizing and understanding the complexities. The chapter attempts to relate each sense to homoplasy. The relationship is important not only for the study of the development of complex structure but also for systematics, where homoplasy is mainly considered as an obstacle to the discernment of evolutionary relationships. One assumption of some cladistic methodologies is that homoplasy is improbable, relative to other sorts of transformation, and that therefore the best-supported phylogeny is the one with the fewest homoplastic events. The chapter analyzes and evaluates this assumption in the case of complex transformations. Eight types of senses or complexity have been identified based on three distinctions (differentiation and configuration, objects and processes, and hierarchical and nonhierarchical complexity). Homoplasy encompasses three types of transformation: reversal, parallelism, and convergence. Each type can take the form of an addition, a deletion, or a modification of a complex developmental process or morphological structure. For each type of complexity and for each type of transformation, structural considerations suggest logic with implications for homoplasy. In general terms, the probability of complex reversal or parallelism ought to depend on type of complexity—especially hierarchical versus nonhierarchical analysis offers a scheme for thinking about complexity and homoplasy, one that may help clarify future discussion.
Outgroup comparison is a special case of the more general use of parsimony in the construction of unrooted trees. The ultimate product of such analyses would be a "global" unrooted tree connecting all species. A direct method for polarising characters is needed to root such a tree. I argue that Nelson's restated biogenetic law is one member of a class of direct methods of character analysis that share the same logical basis: parsimony-based analysis of hierarchically nested, homologous characters. Nested characters may be sets of ontogenetic homologues, linked by ontogenetic transformation, organogenetic transformation or biosynthetic pathways or sets of iterative homologues such as serial homologues and paralogous genes. These methods can be used to decorate a tree with arrows that point towards its root. Phylogenetic loss may result in character distributions that are ambiguous or misleading or for which the methods are inapplicable. The only assumption required beyond those inherent in parsimony-based construction of unrooted trees is that every homology represents a synapomorphy at some level. Nelson's "ontogenetic criterion" does not assume that phylogenetic change occurs exclusively or predominantly through terminal ontogenetic addition.
This chapter examines patterns of evolutionary diversification of behavior among populations of threespine stickleback, Gasterosteus aculeatus, as they invaded freshwater following the recession of the last glaciers and inquires whether population comparisons reveal higher levels of homoplasy than do higher order comparisons. Character polarity can be inferred by comparison with the relatively homogeneous and ubiquitous marine/anadromous fish. This examination of homoplasy revealed through population comparison is limited to this data set because it is the only one in which a large number of population have been characterized behaviorally and in which character polarity can be inferred with a high degree of certainty. The levels of homoplasy observed across freshwater stickleback populations with those observed in comparisons of higher order taxa are contrasted in the chapter. Finally, the chapter examines whether display behavior shows a different level of homoplasy than does nondisplay behavior in population or higher order comparisons. Differences might be expected because displays often incorporate ritualized elements of behavior patterns that appear to have evolved in other contexts and to have subsequently been co-opted for use in the display. The comparisons performed in this study are designed to provide insight into the patterns of evolutionary change at two levels of biological organization and in two major classes of behavior patterns. This chapter will stimulate research on the significance of variation in behavioral homoplasy––its prevalence, and its evolutionary causes.
This chapter provides a statistical assessment of confidence in a phylogenetic tree. The analysis is done with the help of bootstrap procedure. A set of 101 phylogenetic studies was extracted from the TreeBASE data base. The data sets included 50 morphological, 29 restriction fragment length polymorphisms (RFLP), and 22 DNA sequence data sets, ranging in size from 5 to 68 taxa and from 10 to 2226 characters. All studies were on green plants. Each data set was subjected to parsimony analysis using PAUP 3.1. Each data set was then bootstrapped (100 replicates) using heuristic search options. Results reveal several interesting differences among the three different kinds of data. RFLP data sets have the highest average consistency indices (CIs) and retention indices (RIs), the largest number of most parsimonious trees, and the lowest average level of resolution in any given minimal tree. Morphological data sets have the lowest bootstrap support, but their RIs are higher than those for sequence data sets. It can be concluded that the conventional view that confidence is directly related to the level of homoplasy in a data set is not supported by available data from phylogenetic studies. The consistency index is a measure of homoplasy, not robustness. Homoplasy and confidence are two separate issues—not completely independent perhaps, especially in carefully controlled simulation experiments—but effectively so in real data sets.
This chapter discusses the measures of character homoplasy followed by measures of homoplasy for entire data sets or ensembles of characters. It attempts to compare both the standard measures of homoplasy that are in common use in phylogenetics and in many of the more recently developed methods. Several measures of character homoplasy, data set homoplasy, and specialized measures of homoplasy are presented. In phylogenetic analysis, a transformation series among the observed character states is first hypothesized. Homoplasy is inferred by examining the distribution of character states among extant taxa and determining whether or not this distribution can be explained by single changes between plesiomorphic states and relatively apomorphic states based on the hypothesized transformation series, or whether multiple parallel or convergent changes or reversals are required. Homoplasy is fundamentally a property of individual characters. However, the inference of cladistic homoplasy in a phylogenetic analysis depends on the superposition of the character on a phylogenetic tree hypothesis. A basic analysis of the relationship between homoplasy measures and phylogenetic accuracy is presented and a series of recommendations for the use of homoplasy indices are discussed in the chapter.
Comparative systematic studies may use different sets of data or different sets of taxa to evaluate the quality of phylogenetic
data and phylogenetic hypotheses based on levels of homoplasy as implied by the length of minimum length trees. For comparisons
involving diverse arrays of characters and taxa, an appropriate index is required to permit comparisons. Examination of the
number of steps per character (NSC) on minimum length trees for 28 data sets revealed a highly significant positive correlation
between NSC and the number of taxa and, concomitantly, a highly significant negative correlation between the consistency index
(CI) of Kluge and Farris (1969) and the number of taxa. Theoretical expectations from a study of the number of steps on random
and minimum length trees (Archie and Felsenstein, 1989) agree with this finding. Computer simulations using randomly selected
subsets of taxa and characters from the Drosophila data set of Throckmorton (1968) revealed a similar finding. The latter two studies also revealed a negative relationship
between the CI and the number of characters in a study. These findings imply that the CI is not an appropriate index of homoplasy
for comparative taxonomic studies. A new index, the homoplasy excess ratio (HER), is introduced that takes into account the expected increase in overall homoplasy levels with increasing numbers of
taxa in systematic studies. The properties of HER are examined for the 28 data sets taken from the literature and, in conjunction
with the simulations using the Drosophila data set, HER is shown to be more appropriate than CI in comparative taxonomic studies that wish to measure the average level
of homoplasy in data sets involving different groups of taxa or different characters. Because HER is a computationally intensive statistic
to calculate, two estimates are derived and examined. These estimates, the random expected homoplasy excess ratio (REHER) and the homoplasy excess ratio minimum (HERM), can be easily calculated from the formulas of Archie and Felsenstein (1989) and from intrinsic properties of the
data matrix, respectively. HERM is shown to be a better estimator of HER and a linear regression equation is derived to estimate
HER from HERM.
Patterns of variation in levels of homoplasy were explored through statistical analyses of standardized consistency indexes. Data were obtained from 60 recent cladistic analyses of a wide variety of organisms based on several different kinds of characters. Consistency index is highly correlated with the number of taxa included in an analysis, with homoplasy increasing as the number of taxa increases. This observation is compatible with a simple model of character evolution in which 1) the probability of character-state change increases with the total number of branches in a tree and 2) the number of possible states of a character is limited. Consistency index does not show a significant relationship to the number of characters utilized in an analysis or to the taxonomic rank of the terminal taxa. When the relationship between consistency index and number of taxa is taken into account, there is no significant difference between plant and animal data sets in the amount of homoplasy. Likewise, the level of homoplasy in morphological and molecular data sets does not appear to differ significantly, although there are still too few molecular studies to be confident of this result. Future comparisons of consistency indexes, including studies along the lines established here, must take into account the influence of the number of taxa on homoplasy.
It is widely believed that behavior is more evolutionarily labile and/or more difficult to characterize than morphology, and thus that behavioral characters are not as useful as morphological characters for estimating phylogenetic relationships. To examine the relative utility of behavior and morphology for estimating phylogeny, we compared levels of homoplasy for morphological and behavioral characters that have been used in systematic studies. In an analysis of 22 data sets that contained both morphological and behavioral characters we found no significant difference between mean consistency indices (CIs, which measure homoplasy) within data sets for the two types of characters. In a second analysis we compared overall CIs for 8 data sets comprised entirely of behavioral characters with overall CIs for 32 morphological data sets and found no significant difference between the two types of data sets. For both analyses, 95% confidence limits on the difference between the two types of characters indicate that, even if given the benefit of the doubt, morphological characters could not have substantially higher mean CIs than behavioral characters. These results do not support the idea that behavioral characters are less useful than morphological characters for the estimation of phylogeny.
A homolog is a part of the phenotype that is homologous to equivalent parts in other species. A biological homology concept is expected to explain three properties of homologs: 1) the conservation of those features that are used to define a homolog, 2) the individualization of the homolog with regard to the rest of the body, and 3) the uniqueness of homologs, i.e., their specificity for monophyletic groups. The main obstacle to describing a mechanistic basis for homology is the variability of the developmental pathways of undoubtedly homologous characters. However, not all aspects of the developmental pathway are of equal importance. The only organizational features of the developmental system that matter are those that have been historically acquired and cause developmental constraints on the further evolutionary modification of the characters. Two main factors contribute to historically acquired developmental constraints: generative rules of pattern formation and ontogenetic networks. In particular, hierarchical and cyclical inductive networks have the required properties to explain homology. How common such networks are is an open empirical question. The development and variation of pectoral fin hooks in blenniid fishes is presented as a model for the study of a simple ontogenetic network.
Abstract— Dedifferentiation, paedomorphosis, and the insertion and deletion of developmental stages make it impossible to deduce the genealogical hierarchy from only ontogenetic transformation series. Like the outgroup criterion, ontogenetic character precedence is not theory-neutral and to use it to deduce genealogy requires certain assumptions.
If scientists are going to use logically unbeatable theories about the world, they might as well give up natural science and take up religion (Lewontin, 1972: 181).
Phylogenetic trees imply that flowers with a single plane of symmetry (zygomorphic flowers) have evolved several times independently from radially symmetrical (actinomorphic) ancestors within the Asteridae. However, there also appear to have been reversals to actinomorphy. A few evolutionarily derived actinomorphic flowers resemble mutants caused by loss-of-function mutations in genes such as CYCLOIDEA. However, a majority of the shifts from zygomorphy to actinomorphy appear to have entailed a reduction in petal number and flower size, implying a mechanism other than loss of CYCLOIDEA function. Within the Asteridae there appear to be three common forms of zygomorphy. An explanation for the virtual absence of other forms rests on the near universality of the basic orientation of the flower in the Asteridae.
This study was undertaken to determine the range of consistency index (CI) values obtainable from random data sets. We generated multiple random data matrices for each of 49 different matrix sizes ranging from 5 taxa and 4 (binary) characters to 49 taxa and 124 characters. The CI of the minimum-length tree(s) was calculated for each. CIs decreased in a monotonic, nonlinear fashion with addition of either taxa or characters. The influence of addition of taxa was far greater than that of addition of characters, and an interaction effect was recognized. The general curvilinear relation we found between CIs and number of taxa is consistent with results obtained by other authors, but our random data CIs were lower than those of other studies. Mean random CIs varied from 0.70 for the smallest data sets to 0.072 for the largest. Maximum random CIs reached 0.80. A regression through means of random CIs against number of taxa was calculated with a 95% confidence interval. This CI<sub>random</sub> is the minimum value that real data sets should exceed to be considered to contain phylogenetic information. The CIs of real data sets can be adjusted with the CI<sub>random</sub>, and these values are found to meet current criteria for adequate measures of homoplasy. However, the homoplasy indices that are uncorrelated with taxa are also insensitive to internal data set structure, and no current index is adequate for comparison of homoplasy among data sets.
Cladistic analysis of restriction endonuclease cleavage map data, particularly from animal mitochondrial DNA, is considered within a maximum-likelihood framework. The required probability model of evolutionary change is developed from current empirical evidence, and is specific to mtDNA. A large asymmetry is shown to exist between the probabilities of gaining a new site and losing an existing site, with the loss of a site being the much more common event. Since Wagner parsimony assumes that the probabilities of forward and reverse changes are equal, it is a very inefficient estimator of relationships for these data. Dollo parsimony, on the other hand, assumes that the probability of a loss is much greater than that of a gain, an assumption of Dollo parsimony which fits restriction map data well. Dollo parsimony is shown to be a consistent and efficient estimator of phylogeny for mtDNA restriction map data.
We studied the evolution of leaf size, sapling canopy allometry, and related traits in 17 Acer species growing in the understory of temperate deciduous forests, using parsimony methods, randomization tests, and independent contrasts calculated on a phylogeny inferred from nuclear ribosomal internal transcribed spacer (ITS) sequences. Bivariate correlations and multivariate analyses indicated two independent suites of coevolving traits, and the results were robust over a range of alternative phylogenies. The first suite consisted of strong positive correlations among twig thickness, leaf size, inflorescence length, and branch spacing (Corner's rules). Seed size and mature height were also weakly correlated with these traits. The second suite reflected aspects of sapling crown allometry, including crown size, stem diameter, and total leaf area, which appear to be related to shade tolerance. There was a weak negative correlation between sapling crown size and mature height, but no correlation with leaf or seed size. Most correlations were similar in magnitude for ahistorical and independent contrasts analyses, and discrepancies between these two measures were greater in traits with lower levels of convergent evolution. The evolutionary correlations among twig, leaf, seed, inflorescence, and canopy dimensions emphasize the need for integrated theories of evolution and function of these disparate traits.
Dorsoventral asymmetry in flowers is thought to have evolved many times from a radially symmetrical ancestral condition. The first gene controlling floral asymmetry, cycloidea in Antirrhinum, has been isolated. The cycloidea gene is expressed at a very early stage in dorsal regions of floral meristems, where it affects growth rate and primordium initiation. Expression continues through to later stages in dorsal primordia to affect the asymmetry, size and cell types of petals and stamens.
Computer simulations of character-state evolution in 8, 16, 32, and 64 ingroup taxa with a known set of relationships demonstrate that the maximum probability of correct phylogenetic inference increases with the number of variable (or informative) characters and their consistency index and decreases with the number of taxa, when the consistency index has been standardized to eliminate its dependence on the number of taxa. Equations for the probability of correct phylogenetic inference and for the standardized consistency indices (including or excluding autapomorphies) are derived. Given that actual studies based on DNA restriction sites and sequences generate more characters with a higher level of consistency than comparable studies based on morphology, calculations suggest that such molecular studies may often provide a more precise guide to phylogenetic relationships.
Homology describes the inevitable evolutionary phenomenon that the similarity of structures among different organisms is due to the commonality of their descent. This continuity of information is maintained in evolutionary lineages in terms of genes and developmental mechanisms and will retain 'sameness' and retard, funnel and direct evolutionary diversification. Analogous 'sameness' is said to be due to independent, convergent evolution, and also involves similarity of function; the latter is not a necessary condition for structures to be identified as homologous. Here, I suggest that the biological basis for these seemingly disparate kinds of 'sameness' in evolution may in some, or even most, instances not be all that different and may be based on the same principle-the long evolutionary retention of genes, gene interactions and developmental mechanisms. Evolution might recycle and re-recruit similar mechanisms repeatedly during its course, and it often makes do with what is already available to it rather than to newly evolve or reinvent many gene interactions and developmental mechanisms repeatedly. Apparently there is no, or only a negligible, 'genomic cost' or even a selective advantage to maintaining genes and developmental mechanisms for long evolutionary periods of time, even if they are not continuously used in all members along an evolutionary line. Therefore, the biological basis of both homologous traits (those that are evolutionarily always expressed) and homoplasious traits (those that are not always 'on', but are 're-awakened' during evolution) might not be so different, and the distinction between homology and some forms of homoplasy may be somewhat artificial.