Patterns Of Character Evolution Research Articles

An Evolutionary Framework of Acanthaceae Based on Transcriptomes and Genome Skims

Abstract— Acanthaceae is a family of tropical flowering plants with approximately 4900 species. Despite remarkable variation in morphological traits, research on patterns of character evolution has been limited by uncertain relationships among some of the major lineages. We sampled 16 taxa from these major lineages to estimate a phylogenomic framework using a combination of five newly sequenced shotgun genome skims plus seven new and four publicly available transcriptomes. We used OrthoFinder2 to infer a species tree with strong branch support. Except for the placement of Crabbea, our results corroborate the most recent chloroplast and nrITS sequence-based topology. Of 587 single copy loci, 10 were recovered for all 16 species; a RAxML tree estimated from these 10 loci resulted in the same topology as other datasets assembled in this study, with the exception of relationships among three sampled species of Barleria; however, branch support was lower compared to the tree reconstructed using more data. ABBA-BABA tests were conducted to investigate patterns of introgression involving Crabbea; few nucleotides supported alternative topologies. SplitsTree networks of the 587 loci and 6136 orthogroup trees revealed conflict among the branches leading to Andrographideae, Whitfieldieae, and Neuracanthus. A principal components analysis in treespace found no distinct clusters of trees. Our results based on combined genome skim and transcriptome sequences strongly corroborate the previously published chloroplast and nr-ITS-based phylogeny of Acanthaceae with increased resolution among Barlerieae, Andrographideae, Whitfieldieae, and Neuracanthus. This advance in our knowledge of Acanthaceae relationships will allow us to investigate character evolution and other phenomena within this diverse group of plants in studies with increased taxon sampling.

Wood Anatomy of Modern and Fossil Fagales in Relation to Phylogenetic Hypotheses, Familial Classification, and Patterns of Character Evolution

The wood anatomy of fagalean families is summarized. Each family and most genera are wood anatomically distinct and can be distinguished by features such as vessel grouping and arrangement, vessel-ray parenchyma pit type, imperforate element type, ray structure, and axial parenchyma distribution. For each family, we review the published fossil wood record (with particular attention to Cretaceous and Paleogene occurrences) that we consider to be reliably identified on the basis of diagnostic character syndromes, giving insights into their stratigraphic range and former geographic ranges. Fossil woods with characteristics of the Fagaceae (Castaneoideae) occurred as early as the Late Cretaceous (Campanian) of the Northern Hemisphere and were widespread in the Cenozoic. Nothofagaceae wood occurred in the Late Cretaceous and Early Tertiary of Antarctica. Ring-porous Castaneoideae were not common until after the Eocene, reflecting the increase in seasonality that occurred in the Northern Hemisphere at that time. Woods diagnostic of Betulaceae, Juglandaceae, and Myricaceae occurred in the Eocene. With the recognition of Morella Lour. as a genus distinct from Myrica L., we propose two new combinations for fossil woods of Myricaceae. Reliably identified Casuarinaceae wood did not occur until the Miocene. There are no reports of Ticodendraceae fossil wood, although there are reports of fossil woods with its combination of features from the Cretaceous onward, but these are assigned to different families or are of unknown affinities. Most fagalean fossil woods have anatomy similar to that of modern genera, but some Paleogene taxa have combinations of characters not found in present-day genera. We discuss the utility of wood anatomy in assessing phylogenetic relationships within and among families of Fagales, with reference to clades supported by molecular sequence data. Generally, wood anatomical groupings are consistent with recent phylogenetic analyses of the order and of its constituent families. We propose hypotheses about adaptive character evolution in the order based on previously presented phylogenetic relationships inferred from DNA sequence data and the current ecological preferences of individual families.

Phylogenomics Resolves the Relationships within Antennaria (Asteraceae, Gnaphalieae) and Yields New Insights into its Morphological Character Evolution and Biogeography

There is an erratum for this article at: https://doi.org/10.1600/036364420X15959578652451 Abstract—Antennaria are dioecious perennial herbs distributed mainly in the Holarctic Region, with their major center of diversity in the Rocky Mountains of Western North America. The genus comprises 33 known sexual diploid/tetraploid species and at least five polyploid agamic complexes which mostly reproduce by forming asexual seeds. We performed a phylogenetic reconstruction of the 31 sexually-reproducing Antennaria species using a novel target enrichment method that employs custom capture probes designed to work across Asteraceae. Both concatenated and coalescent-based analyses of DNA sequence data from hundreds of nuclear loci recovered Antennaria as a monophyletic group except for the long-disputed species, Antennaria linearifolia, which was recovered outside of the genus. Antennaria was further resolved into three distinct, major lineages. Analysis of ancestral state reconstruction of 12 taxonomically important morphological characters elucidated patterns of character evolution throughout the genus. Estimations of ancestral geographic ranges and molecular dating analyses demonstrated the Rocky Mountain region, including the Vancouverian Province, as the center of origin for the genus Antennaria, around 5.8 MYA. Subsequent dispersals of Antennaria into the Arctic and Appalachian provinces, Canadian provinces, and Eurasia took place roughly 3.2 MYA, 2.4 MYA, and 1.6 MYA, respectively. Biogeographical stochastic mapping indicated that 51.4% of biogeographical events were based on within-area speciation. The remaining 48.6% of the events were divided into two types of dispersals: 1) range expansion dispersals (anagenic, 37%), and 2) founder/jump dispersals (cladogenic, 11.6%). Our results provide a framework for future evolutionary studies of Antennaria, including speciation, origin(s) of polyploidy, and agamospermy in the genus.

New titanosauriform (Dinosauria: Sauropoda) specimens from the Upper Cretaceous Daijiaping Formation of southern China.

Titanosauriform sauropod dinosaurs were once considered rare in the Upper Cretaceous of Asia, but a number of titanosauriforms from this stratigraphic interval have been discovered in China in recent years. In fact, all adequately known Cretaceous Asian sauropods are titanosauriforms, but only a few have been well studied, lending significance to any new anatomical information that can be extracted from Asia’s Cretaceous sauropod record. Here we give a detailed description of some titanosauriform bones recovered recently from the Upper Cretaceous Daijiaping Formation of Tianyuan County, Zhuzhou City, Hunan Province, southern China. The occurrence of this material in Hunan increases the known geographic range of titanosauriforms in eastern Asia. Although all of the specimens discussed in this paper can be assigned to Titanosauriformes at least tentatively, some bones display a limited number of features that are more typical of basal sauropods and/or derived diplodocoids, suggesting complex patterns of character evolution within Neosauropoda.

Patterns of character evolution in phylogenies

Willi Hennig's work has had a profound impact on how we conceive biological systematics and evolution today (Wheeler et al., 2013; Williams et al., 2016). In attempt to establish a novel philosophical and theoretical foundation for systematics, as well as improving its scientific standing, Hennig created new concepts (e.g., autapomorphy, synapomorphy, symplesiomorphy, and semaphoront) and redefined old ones (e.g., monophyly, phylogeny, and relationship) (Rieppel, 2003). Regarding, therefore, the theoretical and practical significance of these concepts and the biological patterns related to them, my main purpose in this letter is eliminating redundancy and increasing precision in the description of the patterns of character evolution in phylogenies, i.e., apomorphy and plesiomorphy. In this way, I (1) endorse the need of a conceptual distinction among autapomorphy, synapomorphy, metapomorphy, and homoplasy, and symplesiomorphy and metaplesiomorphy; (2) introduce the concepts of metapomorphy and metaplesiomorphy within the language of phylogenetic systematics; (3) reinterpret the concept of hemiplasy; and (4) justify why that conceptual distinction is necessary by taking into account its general applicability in theoretical and practical issues of systematics and evolution.

The morphological state space revisited: what do phylogenetic patterns in homoplasy tell us about the number of possible character states?

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, show different 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.

Evolution of leaf blade anatomy in Allium (Amaryllidaceae) subgenus Amerallium with a focus on the North American species

Reconstructing ancestral states is a useful method to understand the pathway and patterns of character evolution and to test specific hypotheses within a phylogenetic context. Using a phylogenetic hypothesis of the subgenus Amerallium and related subgenera based on molecular data, we reconstructed the evolutionary history of leaf blade anatomical characters and identified those characters that are most congruent with phylogenetic relationships. Furthermore, we used these character histories to investigate the evolution of terete leaves and explore a possible correlation between environment and leaf anatomy in the North American species. Sixty-seven North American and Old World species were sampled from all major infrageneric taxa and lineages for transectional leaf anatomy. To provide a phylogenetic framework for interpretation, representatives of Old World Amerallium and related subgenera were added to a published data matrix of North American taxa and ITS, ETS, trnL-F, and rpL32-trnL sequences. Four anatomical characters, namely leaf-blade shape in transection, presence versus absence of palisade mesophyll, distribution and orientation of vascular bundles, and position of laticifer cells, were found to be congruent with phylogenetic relationships and useful diagnostic traits within North American species. Character reconstructions show that terete leaves in North American species evolved from flattened leaves via a possible transition from subterete to terete leaves. Furthermore, terete leaves possess traits that are indicative of possible adaptation to xeric environments. The findings from this study provide valuable information for understanding the evolution of leaf-blade anatomy in North American Allium species.

A phylogenetic analysis of morphological and molecular characters of Boraginaceae: evolutionary relationships, taxonomy, and patterns of character evolution.

The angiosperm family Boraginaceae includes ca. 1600 species distributed among ca. 110 genera. Some floral features are constant within the family, but many vegetative, floral, pollen, and nutlet traits vary. Utilizing 224 species of Boraginaceae and related taxa, five matrices were constructed with various combinations of morphological characters, three chloroplast DNA regions, and one nuclear ribosomal DNA region. Phylogenetic analyses were conducted for these matrices, and patterns of character evolution were examined. Boraginaceae is resolved as monophyletic, with Wellstedia as its sister. Codon is sister to Boraginaceae+Wellstedia. Although most of the investigated morphological characters have a low consistency index, particular character states are synapomorphies for large clades in each of the tribes of the family. In Boraginaceae, the breeding system heterostyly evolved at least 12 times, which is the largest number of origins resolved in any family; therefore Boraginaceae can serve as a model for the evolution and development of heterostyly. Nutlet ornamentation is most diverse in Cynoglosseae and Trichodesmeae, while pollen and floral features are most variable in Boragineae and Lithospermeae. Phylogenetic relationships and patterns of character evolution identified in the present study set the stage for future work creating an updated taxonomic system of Boraginaceae.

Comprehensive Ultrastructure of Kipferlia bialata Provides Evidence for Character Evolution within the Fornicata (Excavata)

Carpediemonas-like organisms (CLOs) are important for understanding the evolutionary history of anaerobic excavates (e.g. diplomonads and parabasalids), especially their cytoskeletal traits and the functions of their modified mitochondria (e.g., hydrogenosomes and mitosomes). Kipferlia bialata is probably the most commonly encountered CLO and has an intriguing molecular phylogenetic position within the Fornicata; however, this species has yet to be described at the ultrastructural level. This study provides a comprehensive account of the ultrastructure of this excavate using light microscopy, SEM, and serial TEM sectioning. The pattern of flagellar transformation observed with SEM confirms that the posterior basal body is the 'eldest', enabling us to emend the numbering system and associated terminology of the flagellar apparatus in excavates. This revised terminology is fundamental for comparing the cytoskeletons of the Excavata supergroup with other eukaryotes. Moreover, K. bialata had several unusal features, such as a hood, a distinct gutter within the ventral groove, and hairs along a single flagellar vane. The ultrastractural data reported here significantly improve our understanding of fornicate morphology, and when placed within a molecular phylogenetic context, these data shed light onto patterns of character evolution within the Excavata.

California Poppy Conundrums: Insights into Relationships within Tribe Eschscholtzieae (Papaveraceae)

We examined the phylogenetic relationships and patterns of character evolution among the California poppies and their relatives (Papaveraceae, Eschscholtzieae) using morphological comparisons and parsimony and likelihood-based phylogenetic analyses of two chloroplast and two nuclear DNA regions, including 14-3-3-like, a phylogenetically informative nuclear DNA region developed for this research. Each of the three genera in the tribe (Dendromecon, Eschscholzia, and Hunnemannia) is strongly supported as monophyletic, but not all species of Eschscholzia display monophyly based on molecular data. Examination of biogeographic patterns indicates that dispersal to island habitats occurred more than twice in the tribe. Phylogenetic reconstruction of the evolution of chromosome number suggests that there were several polyploidy events within the tribe and likely one or more aneuploid events within Eschscholzia. Based on the results presented here, the subspecies of both Eschscholzia californica and Eschscholzia lemmonii will be promoted to specific status. Additionally, the study provides evidence supporting recognition of two new species of desert Eschscholzia.

Body-form Evolution in the Scincid Lizard Clade Lerista and the Mode of Macroevolutionary Transitions

The scincid lizard clade Lerista provides an exceptional model for studying the mode of substantial evolutionary transformations, comprising more than 90 species displaying a remarkable variety of body forms. Patterns of character evolution in this clade, inferred from reconstructed ancestral states, are at least partly consistent with the correlated progression model of macroevolutionary change. At each stage in the transition to a highly elongate, limb-reduced body plan, alterations to the lengths of the forelimb and hind limb are accompanied by compensatory changes in snout-vent length (or vice versa), preserving locomotory ability. Nonetheless, there is evidence for moderate dissociation of hind limb evolution in some lineages, while tail length has evolved effectively independently of the substantial alterations to the lengths of the body and limbs. This indicates a significant role of evolutionary and developmental modularity in the divergence of body form within Lerista, and emphasises the potential variability of the strength of functional constraints within organisms and among lineages. Trends toward a highly elongate, functionally limbless body plan may be attributed primarily to a combination of the interdependence of changes in snout-vent length and limb lengths and the very low probability of re-elaborating structurally reduced limbs. Similar asymmetries in the probabilities of interrelated phenotypic changes may be a significant cause of evolutionary trends resulting in the emergence of higher taxa.

Monographing micromolluscs: A case study on Scissurellidae s.l. (Vetigastropoda)

The last taxonomic monographs of micromolluscs (size less than 5 mm) of worldwide scope date back to the turn of the 19th/20th century, prior to the invention of the scanning electron microscope (SEM). In the present study, experiences from the preparation of a monograph on worldwide Scissurellidae s.l., a gastropod taxon comprising minute members plus an overview of this taxon, are provided. The literature is mercifully brief with some 650 references tracked, equal to approximately 4.6 references per species. Relying on secondary resources has proven to be problematic, and all primary taxonomic sources have to be consulted. The internet has made some searches easier, but some invalid names have surfaced. Generic concepts have often not been evaluated phylogenetically, and family-level micromollusc taxa may well be para- or even polyphyletic, which needs to be evaluated early on. Although underdetermined data matrices from shell morphology are problematic, they do provide some information on overall patterns of character evolution. The usual practice of only examining a single specimen by SEM is fraught with problems as it does not permit the identifi cation of intraspecifi c and ontogenetic variability. Old type material should be examined now that environmental and variable pressure SEMs are available. As micromolluscs are most susceptible to adverse environmental and storage conditions, upgrade of storage of micromolluscan types should be given highest priority. At least 89 species (conservative estimate) remain to be described. The Atlantic is less diverse in both species as well as genera. Tropical and temperate waters hold approximately the same number of species, while the polar oceans have a much lower diversity. The geographic coverage of available material is primarily driven by contemporary sampling initiatives, and no sampling bias due to the longer history of collecting in European can be detected. Sampling in general and available material for Scissurellidae declines with depth; only ten lots are known from greater than 3,000 m. Scissurellidae are proportionally less frequent in shallow waters, and are overrepresented on the upper slope (300–1,000 m). Labor-intensive procedures are mainly sorting of micromollusc samples, and digital processing (cut-out) of SEM images.

RbcL Phylogeny and Character Evolution in Polygonaceae

Abstract Phylogenetic relationships within Polygonaceae, with an emphasis on Polygonum and segregate genera (e.g., Emex, Persicaria, Polygonella), are investigated using sequence data from the chloroplast gene rbcL. The results show the currently recognized subfamilies are likely not monophyletic. Polygonum as currently recognized is paraphyletic. Three strongly supported clades of Polygonum s.l. were found. Contained within these three clades of Polygonum s.l. are representatives of Atraphaxis, Bistorta, Koenigia and Persicaria. Other strongly supported clades found are Coccoloba, Eriogonum, Fagopyrum, Rumex and Triplaris. Patterns of character evolution were studied by mapping characters onto the phylogeny. A woody habit likely evolved multiple times within the family (in Atraphaxis, Koenigia, Muehlenbeckia, Polygonella and in the ancestor to the Eriogonum–Brunnichia clade). Quincuncial aestivation likely evolved early in the history of the family with four subsequent losses in the Rumex–Oxyria clade, M...

Phylogeny of Habronattus jumping spiders (Araneae: Salticidae), with consideration of genital and courtship evolution

Abstract. DNA sequences from the mitochondrial (including ND1, 16S) and nuclear (EF‐1α) genomes of about ninety‐four species were obtained to reconstruct phylogenetic relationships of Habronattus jumping spiders. Maximum parsimony trees were sought with both separate (mitochondrial, nuclear) and combined analyses; maximum likelihood trees were sought with both separate (ND1, 16S, EF‐1α introns, EF‐1α exons) and combined (mitochondrial, nuclear) analyses. All analyses agreed on some fundamental aspects of the tree, including the monophyly of the previously recognized agilis, amicus, dorotheae and americanus species groups. The deep phylogenetic structure is well resolved, placing the agilis, amicus, tranquillus and dorotheae groups basally. Several other previously unrecognized clades were well supported, including a newly formulated decorus group. The large group of species with modified male first and third legs was supported as monophyletic except for the surprising placement elsewhere of three species of the group. The phenotypic similarities between these three and the others are so detailed and precise that convergence in ornamentation can probably be ruled out. There are hints of phylogenetically distant genetic introgression involving the coecatus group. The combination Habronattus paratus is restored based on the species falling within Habronattus. Regarding patterns of character evolution, there was consistent support for the basal placement of several species groups with a long embolus, suggesting that there were more evolutionary reductions in embolus length than postulated in a previous morphological phylogeny. This is in accord with the expectation that there is a bias to an overly conservative interpretation of a character's evolution if it is interpreted on a phylogeny based in part on that same character. In contrast, the molecular phylogeny did not suggest any instances of the evolutionary transformation of one complex style of courtship into another, a possibility that could have been difficult to detect using the morphological phylogeny because of the same bias to conservativism.

Homoplasy and Developmental Constraint: A Model and an Example from Plants1

Much attention has been paid to the role of developmental information in estimating phylogenetic relationships and, more recently, to the use of phylogenies 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 orientation and underlying mechanisms of differentiation.

Angiosperm wood evolution and the potential contribution of paleontological data

Wood anatomy is often viewed as a source of independent data that may be used to assess evolutionary relationships among angiosperms. Comparative anatomical studies document suites of correlated characters that have been interpreted as general evolutionary trends, of which several have been asserted to be irreversible. Paleobotanical data summarized by Wheeler and Baas provide broad chronological corroboration of some wood anatomical trends, such as evolution from scalariform to simple perforation plates and long to short vessel elements. However, the focus on general evolutionary trends rather than on analyzing character distribution patterns in a cladistic phylogenetic context obscures a more detailed understanding of the evolution of wood anatomical features. Patterns of character evolution, including the assertions of irreversibility, need to be tested through cladistic analyses. In this paper selected wood anatomical features from families of Magnoliidae and “lower” Hamamelididae are summarized and mapped onto previously published cladograms as a preliminary means of testing previous hypotheses of wood evolution. The results show that many of the characters are homoplasious and have evolved both in accord with, and counter to, the hypothesized general trends in different groups of flowering plants. In general, changes that confirm generalized trends are more common than changes that are counter to those trends. Future studies should combine wood anatomical characters with other features as part of a cladistic analysis. Fossil woods have not yet contributed significantly to phylogenetic studies, but in the very few cases where they have been linked to fossil reproductive structures, the woods have provided a better understanding of wood anatomy in early members of some families. Data from fossil wood expand the diversity of anatomical structure known in some angiosperm taxa and thus provide additional evidence that might be used in phylogenetic analyses. Fossil woods have the greatest potential to affect phylogenetic analyses where they can be linked to other fossil organs. The best chance for establishing such a linkage is through the study of fossil charcoalified woods that co-occur with other dispersed mesofossils.

Evolution of Pigment Pattern Development in Centrarchid Fishes

Pigmentation patterns are commonly assumed to be difficult characters to use in phylogenetic studies because of pattern variability within individuals and species. Most studies, however, have focused on the variability of adult pigmentation pattern, where pattern element homologies are most difficult to recognize. By observing the development of pigmentation patterns in larval, juvenile, and adult centrarchids, the homologous elements of the lateral barring pattern have been hypothesized. This has permitted the comparison of pattern ontogenies in a phylogenetic context. Although pigmentation is often disregarded as a source of characters containing historical information, the congruence of many of these characters with a phylogeny of centrarchids suggests their utility. The ontogenies of pigmentation patterns in 26 centrarchid species are described. Several equally parsimonious patterns of character evolution are implied by the phylogeny, and these are discussed. Pigmentation diversity among adult centrarchids is produced by the alteration of homologous components and rarely by the addition of novel characteristics. A common mechanism underlying pattern formation is suggested by pigmentation similarities among centrarchids.

Phylogenetic interpretation of ontogenetic change: sorting out the actual and artefactual in an empirical case study of centrarchid fishes

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 × 10 36 trees possible for centrarchids. It was found for these data that terminal change accounts for c. 75% of the character state change. This suggests either that early ontogeny is conserved in evolution or that interpretation and classification of evolutionary changes in ontogeny is biased in part by the way that characters are recognized, delimited and coded. It was found that ontogenetic interpretation is influenced by two levels of homology decision: an initial decision involving delimitation of the character (the ontogenetic sequence), and the subsequent recognition of homologous components of developmental sequences. Recognition of phylogenetic homology among individual components of developmental sequences is necessary for interpretation of evolutionary changes in ontogeny as either terminal or non-terminal. If development is the primary criterion applied in recognizing individual homologies among parts of ontogenetic sequences, the only possible interpretation of phylogenetic differences is that of terminal change. If homologies of the components cannot be ascertained, recognition of the homology of the developmental sequence as a whole will result in the interpretation of evolutionary differences as substitutions. Particularly when the objective of a study is to discover how ontogeny has evolved, criteria in addition to ontogeny must be used to recognize homology. Interpretation is also dependent upon delimitation within an ontogenetic sequence. This is in part a function of the way that an investigator 'sees' and codes characters. Binary and multistate characters influence interpretation differently and predictably. The use of ontogeny for determining phylogenetic polarity as previously proposed rests on the assumptions that ancestral ontogenies are conserved and that character evolution occurs predominantly through terminal addition. It was found for these data that terminal addition may comprise a maximum of 51.9% of the total character state change. It is concluded that the ontogenetic criterion is not a reliable indicator of phylogenetic polarity. Process and pattern data are collected simultaneously by those engaged in comparative morphological studies of development. The set of alternative explanatory processes is limited in the process of observing development. These form necessary starting points for the research of developmental biologists. Separating 'empirical' results from interpretational influences requires awareness of potential biases in the course of character selection, coding and interpretation. Consideration of the interpretational problems involved in identifying and classifying phylogenetic changes in ontogeny leads to a re-evaluation of the purpose, usefulness and information conveyed by the current classification system. It is recommended that alternative classification schemes be pursued.

Phylogenetic interpretation of ontogenetic change: sorting out the actual and artefactual in an empirical case study of centrarchid fishes

Abstract 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 × 10 36 trees possible for centrarchids. It was found for these data that terminal change accounts for c. 75% of the character state change. This suggests either that early ontogeny is conserved in evolution or that interpretation and classification of evolutionary changes in ontogeny is biased in part by the way that characters are recognized, delimited and coded. It was found that ontogenetic interpretation is influenced by two levels of homology decision: an initial decision involving delimitation of the character (the ontogenetic sequence), and the subsequent recognition of homologous components of developmental sequences. Recognition of phylogenetic homology among individual components of developmental sequences is necessary for interpretation of evolutionary changes in ontogeny as either terminal or non-terminal. If development is the primary criterion applied in recognizing individual homologies among parts of ontogenetic sequences, the only possible interpretation of phylogenetic differences is that of terminal change. If homologies of the components cannot be ascertained, recognition of the homology of the developmental sequence as a whole will result in the interpretation of evolutionary differences as substitutions. Particularly when the objective of a study is to discover how ontogeny has evolved, criteria in addition to ontogeny must be used to recognize homology. Interpretation is also dependent upon delimitation within an ontogenetic sequence. This is in part a function of the way that an investigator 'sees' and codes characters. Binary and multistate characters influence interpretation differently and predictably. The use of ontogeny for determining phylogenetic polarity as previously proposed rests on the assumptions that ancestral ontogenies are conserved and that character evolution occurs predominantly through terminal addition. It was found for these data that terminal addition may comprise a maximum of 51.9% of the total character state change. It is concluded that the ontogenetic criterion is not a reliable indicator of phylogenetic polarity. Process and pattern data are collected simultaneously by those engaged in comparative morphological studies of development. The set of alternative explanatory processes is limited in the process of observing development. These form necessary starting points for the research of developmental biologists. Separating 'empirical' results from interpretational influences requires awareness of potential biases in the course of character selection, coding and interpretation. Consideration of the interpretational problems involved in identifying and classifying phylogenetic changes in ontogeny leads to a re-evaluation of the purpose, usefulness and information conveyed by the current classification system. It is recommended that alternative classification schemes be pursued.

SYSTEMATIC IMPLICATIONS OF CHLOROPLAST DNA VARIATION IN THE SUBTRIBE MICROSERIDINAE (ASTERACEAE: LACTUCEAE)

Phylogenetic relationships among six of the seven currently recognized genera of the subtribe Microseridinae were examined using comparative restriction site mapping of the chloroplast genome. Complete cleavage maps of 17 enzymes were constructed for 35 of the 46 species in the subtribe and six representative outgroup species from four other subtribes of the Lactuceae. A total of 373 restriction site mutations was detected, 180 of which were phylogenetically informative. The chloroplast DNA mutations were used to generate phylogenetic trees using Dollo, Wagner, and weighted parsimony, and the resulting monophyletic groups were evaluated by the bootstrap method. The results indicate that the Microseridinae is paraphyletic because Stephanomeria is nested within the six core genera of the subtribe. Five of the genera of the Microseridinae are monophyletic, whereas Microseris is paraphyletic because one of its species, M. lindleyi, is more closely related to Agoseris and Nothocalais. The distant relationship of M. lindleyi to the rest of the species of Microseris is enigmatic, especially in view of its known involvement in the origin of two allotetraploid species, M. decipiens and M. heterocarpa. The taxonomic implications of these results lead to a revised classification of Microseris in which the genus Uropappus is revived to accommodate M. lindleyi, and a new genus, Stebbinsoseris, is described to include the allotetraploids. The cpDNA phylogeny is used to evaluate the patterns of character evolution within the Microseridinae, as well as to test previous hypotheses that differences in generation time result in unequal rates of chloroplast DNA evolution.