Transition Confidence and Modified Mean Values: Confidence Measures for Hypotheses of Character State Transition between Nodes and Ancestral State Optimizations

A measure is introduced to quantify the reliability of character state transitions and character state stasis (lack of character state change between nodes). The mean value of a character state at an internal node is altered to obtain a measure termed the modified mean. Modified mean values at connecting nodes are employed to determine the support for hypotheses of character state transition/stasis between the nodes. The lowest of the two neighboring modified mean values implied by an hypothesis of character state transition/stasis is used as a direct measure of support for that hypotheses of character state transformation or stasis between the respective nodes.     

MEASURING EVOLUTIONARY CONSTRAINTS: A MARKOV MODEL FOR PHYLOGENETIC TRANSITIONS AMONG SEED DISPERSAL SYNDROMES

I introduce a Markov probabilistic model of transitions among discrete morphological states as a method for describing and testing nonrandom patterns of evolutionary change. The Markov model assumes one-generational dependency, i.e., that the future direction of evolutionary change depends on the current morphology of a species, not on any history of changes. This model is very flexible, allowing for any number of discrete states to describe morphology, yet permit rigorous testing of even complex evolutionary hypotheses. I apply this model to changes in seed dispersal mechanisms within 571 genera of Neotropical plants, using cladistic methods to infer the ancestral and derived states within each genus. I then test a series of progressively more complex hypotheses about the constraints that might shape the patterns of observed evolutionary transitions: 1) no transition constraints; 2) all dispersal mechanisms are equally labile evolutionarily; 3) the probability of particular evolutionary transitions among dispersal mechanisms depends on the descendant state but not on the ancestral state; 4) transition probabilities differ among pairs of dispersal mechanisms, but are reciprocal within such pairs. More complex hypotheses matched the data significantly better than did simpler hypotheses. However, only one of the hypotheses (reciprocal transitions) fit the observed data and then only for the most cautious interpretation of the frequencies of transitions within genera. These results suggest that evolutionary transitions among major adaptive syndromes are indeed ordered, and the observed patterns of transitions suggest possible reasons for such macroevolutionary structure.     

THE DIVERSITY AND EVOLUTION OF BATESIAN MIMICRY IN PAPILIO SWALLOWTAIL BUTTERFLIES

Papilio swallowtail butterflies exhibit a remarkable diversity of Batesian mimicry, manifested in several sex-limited and polymorphic types. There is little understanding of how this diversity is distributed within Papilio , and how different mimicry types have evolved in relation to each other. To answer these questions, I present a graphical model that connects various mimicry types by hypothetical character state changes within a phylogenetic framework. A maximum likelihood analysis of evolution of mimicry types on the Papilio phylogeny showed that sexually monomorphic mimicry and female-limited mimicry have evolved repeatedly but predominantly independently in different clades. However, transitions between these mimicry types are rarely observed. The frequency distribution of character state changes was skewed in favor of the evolution of mimicry, whereas many theoretically plausible character state changes, especially evolutionary loss of mimicry, were not evident. I discuss these findings in relation to studying the tempo of evolutionary change, loss of traits, and directionality and connectivity among character states. The pathway approach and phylogenetic patterns of mimicry demonstrated in Papilio are useful to test novel hypotheses regarding the diversity and evolutionary directionality of Batesian mimicry in other systems.     

Trait-based species richness: ecology and macroevolution

Understanding the origins of species richness patterns is a fundamental goal in ecology and evolutionary biology. Much research has focused on explaining two kinds of species richness patterns: (i) spatial species richness patterns (e.g. the latitudinal diversity gradient), and (ii) clade-based species richness patterns (e.g. the predominance of angiosperm species among plants). Here, I highlight a third kind of richness pattern: trait-based species richness (e.g. the number of species with each state of a character, such as diet or body size). Trait-based richness patterns are relevant to many topics in ecology and evolution, from ecosystem function to adaptive radiation to the paradox of sex. Although many studies have described particular trait-based richness patterns, the origins of these patterns remain far less understood, and trait-based richness has not been emphasised as a general category of richness patterns. Here, I describe a conceptual framework for how trait-based richness patterns arise compared to other richness patterns. A systematic review suggests that trait-based richness patterns are most often explained by when each state originates within a group (i.e. older states generally have higher richness), and not by differences in transition rates among states or faster diversification of species with certain states. This latter result contrasts with the widespread emphasis on diversification rates in species-richness research. I show that many recent studies of spatial richness patterns are actually studies of trait-based richness patterns, potentially confounding the causes of these patterns. Finally, I describe a plethora of unanswered questions related to trait-based richness patterns.     

TESTING HYPOTHESES OF NEURAL EVOLUTION IN GYMNOTIFORM ELECTRIC FISHES USING PHYLOGENETIC CHARACTER DATA

In this paper, we propose a method to test alternative hypotheses of phenotypic evolution. The method compares patterns observed in phylogenetic character data with patterns expected by explicit models of evolutionary process. Observed patterns of character-state diversity are assessed from four properties of character-state change derived from a phylogenetic analysis: the sequence and correlation of transformations on a cladogram and the spatial and functional localization of these transformations to parts of an organism. Patterns expressed in terms of the localization of transformations are compared with the expectations of null models that the number of transformations is proportional to measures of size or complexity. Deviations from the values expected by the null models are then compared with qualitative expectations of the models. The method is applied to characters in the nervous system of gymnotiform electric fishes. Patterns in the diversity of 63 reconstructed character-state changes are compared with the expectations of 10 published models of neural evolution. A total of 63 expectations are reviewed, of which 33 (52%) are found to be consistent with the gymnotiform neural data. In general, the models reviewed are not successful at making global predictions, in part because they have been cast in excessively general terms. The data support the conclusion that evolution in the nervous system of gymnotiforms has involved a mosaic of processes, each operating differentially on functional and developmental systems and at different spatial and temporal scales. The results also indicate that more refined models are required, each making more explicit predictions.     

Tempo does not correlate with mode in the fossil record

The dominating view of evolution based on the fossil record is that established species remain more or less unaltered during their existence. Substantial evolution is on the other hand routinely reported for contemporary populations, and most quantitative traits show high potential for evolution. These contrasting observations on long‐ and short‐time scales are often referred to as the paradox of stasis, which rests on the fundamental assumption that periods of morphological stasis in the fossil record represent minimal evolutionary change. Investigating 450 fossil time series, I demonstrate that the nonaccumulating morphological fluctuations during stasis travel similar distances in morphospace compared to lineages showing directional change. Hence, lineages showing stasis are commonly undergoing considerable amounts of evolution, but this evolution does not accumulate to produce large net evolutionary changes over time. Rates of evolutionary change across modes in the fossil record may be more homogenous than previously assumed and advocated, supporting the claim that substantial evolution is not exclusively or causally linked to the process of speciation. Instead of exemplifying minimal evolution, stasis likely represents information on the dynamics of the adaptive landscape on macroevolutionary time scales, including the persistence of adaptive zones and ecological niches over millions of years.     

Emergent and effective properties in ecology and evolution

Emergent properties are often discussed in arguments concerning relationships among different levels. However, the different definitions of emergent properties sometimes confuse the arguments about macro-level phenomena, since some authors regard emergent properties not only as observable global patterns but as properties that affect and cause change in ecological and evolutionary processes. Thus it is important to distinguish higher-level or larger-scale properties that can influence particular ecological and evolutionary processes from those that cannot. I call the former properties effective properties. I gave examples that show why the distinctions between effective and non-effective properties are important.

     

EVOLUTIONARY CONSTRAINT AND ECOLOGICAL CONSEQUENCES

One of the most important shifts in evolutionary biology in the past 50 years is an increased recognition of sluggish evolution and failures to adapt, which seem paradoxical in view of abundant genetic variation and many instances of rapid local adaptation. I review hypotheses of evolutionary constraint (or restraint), and suggest that although constraints on individual characters or character complexes may often reside in the structure or paucity of genetic variation, organism‐wide stasis, as described by paleontologists, might better be explained by a hypothesis of ephemeral divergence, according to which the spatial or temporal divergence of populations is often short‐lived because of interbreeding with nondivergent populations. Among the many consequences of acknowledging evolutionary constraints, community ecology is being transformed as it takes into account phylogenetic niche conservatism and the strong imprint of deep history.     

Ecological bistability and evolutionary reversals under asymmetrical competition

Abstract How does the process of life‐history evolution interplay with population dynamics? Almost all models that have addressed this question assume that any combination of phenotypic traits uniquely determine the ecological population state. Here we show that if multiple ecological equilibria can exist, the evolution of a trait that relates to competitive performance can undergo adaptive reversals that drive cyclic alternation between population equilibria. The occurrence of evolutionary reversals requires neither environmentally driven changes in selective forces nor the coevolution of interactions with other species. The mechanism inducing evolutionary reversals is twofold. First, there exist phenotypes near which mutants can invade and yet fail to become fixed; although these mutants are eventually eliminated, their transitory growth causes the resident population to switch to an alternative ecological equilibrium. Second, asymmetrical competition causes the direction of selection to revert between high and low density. When ecological conditions for evolutionary reversals are not satisfied, the population evolves toward a steady state of either low or high abundance, depending on the degree of competitive asymmetry and environmental parameters. A sharp evolutionary transition between evolutionary stasis and evolutionary reversals and cycling can occur in response to a smooth change in ecological parameters, and this may have implications for our understanding of size‐abundance patterns.     

TESTING FOR UNEQUAL AMOUNTS OF EVOLUTION IN A CONTINUOUS CHARACTER ON DIFFERENT BRANCHES OF A PHYLOGENETIC TREE USING LINEAR AND SQUARED-CHANGE PARSIMONY: AN EXAMPLE USING LESSER ANTILLEAN ANOLIS LIZARDS

Although a large body of work investigating tests of correlated evolution of two continuous characters exists, hypotheses such as character displacement are really tests of whether substantial evolutionary change has occurred on a particular branch or branches of the phylogenetic tree. In this study, we present a methodology for testing such a hypothesis using ancestral character state reconstruction and simulation. Furthermore, we suggest how to investigate the robustness of the hypothesis test by varying the reconstruction methods or simulation parameters. As a case study, we tested a hypothesis of character displacement in body size of Caribbean Anolis lizards. We compared squared-change, weighted squared-change, and linear parsimony reconstruction methods, gradual Brownian motion and speciational models of evolution, and several resolution methods for linear parsimony. We used ancestor reconstruction methods to infer the amount of body size evolution, and tested whether evolutionary change in body size was greater on branches of the phylogenetic tree in which a transition from occupying a single-species island to a two-species island occurred. Simulations were used to generate null distributions of reconstructed body size change. The hypothesis of character displacement was tested using Wilcoxon Rank-Sums. When tested against simulated null distributions, all of the reconstruction methods resulted in more significant P-values than when standard statistical tables were used. These results confirm that P-values for tests using ancestor reconstruction methods should be assessed via simulation rather than from standard statistical tables. Linear parsimony can produce an infinite number of most parsimonious reconstructions in continuous characters. We present an example of assessing the robustness of our statistical test by exploring the sample space of possible resolutions. We compare ACCTRAN and DELTRAN resolutions of ambiguous character reconstructions in linear parsimony to the most and least conservative resolutions for our particular hypothesis.     

NULL MODELS FOR THE NUMBER OF EVOLUTIONARY STEPS IN A CHARACTER ON A PHYLOGENETIC TREE

Random trees and random characters can be used in null models for testing phylogenetic hypothesis. We consider three interpretations of random trees: first, that trees are selected from the set of all possible trees with equal probability; second, that trees are formed by random speciation or coalescence (equivalent); and third, that trees are formed by a series of random partitions of the taxa. We consider two interpretations of random characters: first, that the number of taxa with each state is held constant, but the states are randomly reshuffled among the taxa; and second, that the probability each taxon is assigned a particular state is constant from one taxon to the next. Under null models representing various combinations of randomizations of trees and characters, exact recursion equations are given to calculate the probability distribution of the number of character state changes required by a phylogenetic tree. Possible applications of these probability distributions are discussed. They can be used, for example, to test for a panmictic population structure within a species or to test phylogenetic inertia in a character's evolution. Whether and how a null model incorporates tree randomness makes little difference to the probability distribution in many but not all circumstances. The null model's sense of character randomness appears more critical. The difficult issue of choosing a null model is discussed.     

Character Displacement in Evolutionary Time

Patterns of distribution of morphology in the fossil recordshould be examined more rigorously to evaluate the relativeeffectiveness of alternative evolutionary models and to integratethe dimension of true evolutionary time more directly with evolutionarytheory. Grant (1972) has discussed three main problems in the detectionof character displacement: we must assume that sympatry followedallopatry, that the state in allopatry represents the static,pre-contact state, and that there are no other reasons accountingfor differences within a species in allopatric and sympatriczones. These problems can be largely avoided with suitable paleoiitologicaldata. In an example involving the coincident 10 million-year historiesof two congeneric species of Devonian trilobites, the one knowninstance of sympatry reveals marked divergent shifts in onespecies and a "mixed" reaction of convergent, divergent, andneutral shifts in the other species. The characters undergoingthese shifts are largely those which (i) serve as specific differentia,and (ii) show the most change within one of the species overits entire history. This suggests that character displacementmay be simply a magnified microcosm of a general pattern ofinteraction between two species even when allopatric, providedthat allopatry is sustained through competitive exclusion.     

Homology a personal view on some of the problems

There are many problems relating to defining the terminology used to describe various biological relationships and getting agreement on which definitions are best. Here, I examine 15 terminological problems, all of which are current, and all of which relate to the usage of homology and its associated terms. I suggest a set of definitions that are intended to be totally consistent among themselves and also as consistent as possible with most current usage.     

Constraints on the morphological evolution of marsupial shoulder girdles

Throughout their evolutionary histories, marsupial mammals have been taxonomically and morphologically less diverse than their sister taxa the placentals. Because of this, it has been proposed that the evolution of marsupials has been constrained by the functional requirements of their mode of reproduction. Marsupials give birth after short gestation times to immature neonates that immediately crawl, under the power of their precociously developed shoulder girdles, to the teat where they attach and complete their early development. Using a novel approach incorporating adult and embryological morphological data, this study is the first to both: (1) statistically support adult patterns of morphological divergence consistent with the constraint hypothesis, and (2) identify ontogenetic patterns of morphological change that demonstrate that the constraint was responsible, at least in part, for their formation. As predicted by the marsupial constraint, the shoulder girdles of adult marsupials are less diverse than those of adult placentals, and adult marsupial scapulae are less morphologically diverse than adult marsupial pelves. Furthermore, marsupials that complete an extensive crawl to the teat are restricted to a common pattern of ontogenetic scapular shape change, strongly supporting the hypothesis that the morphological development of the marsupial scapula has been limited evolutionarily by its obligate role in the crawl to the teat. Because this study establishes that ontogenetic and evolutionary morphological change is correlated within mammalian scapulae, it is probable that the marsupial constraint also restricted the morphological divergence of the scapula over evolutionary time by limiting ontogenetic change in the scapula. These findings, coupled with the importance of the shoulder girdle in mammalian locomotor specialization, support the conclusion that the low morphological diversity of marsupial forms over evolutionary time could be directly due to the constraint on marsupial morphological evolution caused by the functional requirements of the crawl to the teat.     

Mosaic evolution,preadaptation, and the evolution of evolvability in apes

A major goal in postsynthesis evolutionary biology has been to better understand how complex interactions between traits drive movement along and facilitate the formation of distinct evolutionary pathways. I present analyses of a character matrix sampled across the haplorrhine skeleton that revealed several modules of characters displaying distinct patterns in macroevolutionary disparity. Comparison of these patterns to those in neurological development showed that early ape evolution was characterized by an intense regime of evolutionary and developmental flexibility. Shifting and reduced constraint in apes was met with episodic bursts in phenotypic innovation that built a wide array of functional diversity over a foundation of shared developmental and anatomical structure. Shifts in modularity drove dramatic evolutionary changes across the ape body plan in two distinct ways: (1) an episode of relaxed integration early in hominoid evolution coincided with bursts in evolutionary rate across multiple character suites; (2) the formation of two new trait modules along the branch leading to chimps and humans preceded rapid and dramatic evolutionary shifts in the carpus and pelvis. Changes to the structure of evolutionary mosaicism may correspond to enhanced evolvability that has a “preadaptive” effect by catalyzing later episodes of dramatic morphological remodeling.     

The information content of a character under a Markov model of evolution

The rate of evolutionary change associated with a character determines its utility for the reconstruction of phylogenetic history. For a given age of lineage splits, we examine the information content of a character to assess the magnitude and range of an optimal rate of substitution. On the one hand an optimal transition rate must provide sufficiently many character changes to distinguish subclades, whereas on the other hand changes must be sufficiently rare that reversals on a single branch (and hence homoplasy) are uncommon. In this study, we evolve binary characters over three tree topologies with fixed branch lengths, while varying transition rate as a parameter. We use the character state distribution obtained to measure the "information content" of a character given a transition rate. This is done with respect to several criteria-the probability of obtaining the correct tree using parsimony, the probability of infering the correct ancestral state, and Shannon-Weaver and Fisher information measures on the configuration of probability distributions. All of the information measures suggest the intuitive result of the existence of optimal rates for phylogeny reconstruction. This nonzero optimum is less pronounced if one conditions on there having been a change, in which case the parsimony-based results of minimum change being the most informative tends to hold.     

Diversification on an ecologically constrained adaptive landscape

We used phylogenetic analysis of body-size ecomorphs in a crustacean species complex to gain insight into how spatial complexity of ecological processes generates and maintains biological diversity. Studies of geographically widespread species of Hyalella amphipods show that phenotypic evolution is tightly constrained in a manner consistent with adaptive responses to alternative predation regimes. A molecular phylogeny indicates that evolution of Hyalella ecomorphs is characterized by parallel evolution and by phenotypic stasis despite substantial levels of underlying molecular change. The phylogeny suggests that species diversification sometimes occurs by niche shifts, and sometimes occurs without a change in niche. Moreover, diversification in the Hyalella ecomorphs has involved the repeated evolution of similar phenotypic forms that exist in similar ecological settings, a hallmark of adaptive evolution. The evolutionary stasis observed in clades separated by substantial genetic divergence, but existing in similar habitats, is also suggestive of stabilizing natural selection acting to constrain phenotypic evolution within narrow bounds. We interpret the observed decoupling of genetic and phenotypic diversification in terms of adaptive radiation on an ecologically constrained adaptive landscape, and suggest that ecological constraints, perhaps acting together with genetic and functional constraints, may explain the parallel evolution and evolutionary stasis inferred by the phylogeny.     

Backyard evolutionary biology: Investigating local flowers brings learning to life

Inquiry‐based learning allows students to actively engage in and appreciate the process of science. As college courses transition to online instruction in response to COVID‐19, incorporating inquiry‐based learning is all the more essential for student engagement. However, with the cancelation of in‐person laboratory courses, implementing inquiry can prove challenging for instructors. Here, I describe a case that exemplifies a strategy for inquiry‐based learning and can be adapted for use in various course modalities, from traditional face‐to‐face laboratory courses to asynchronous and synchronous online courses. I detail an assignment where students explore the developmental basis of morphological evolution. Flowers offer an excellent example to address this concept and are easy for students to access and describe. Students research local flowering plants, collect and dissect flower specimens to determine their whorl patterns, and generate hypotheses to explain the developmental genetic basis of the patterns identified. This task allows students to apply their scientific thinking skills, conduct guided exploration in nature, and connect their understanding of the developmental basis of evolutionary change to everyday life. Incorporating inquiry using readily available, tangible, tractable real‐world examples represents a pragmatic and effective model that can be applied in a variety of disciplines during and beyond COVID‐19.     

Relationships among development, ecology, and morphology in the evolution of Echinoderm larvae and life cycles

The evolution of life cycles involves transitions between discrete states in one or more of the characters that comprise a developmental pattern. In this paper, we examine three of the major life cycle characters and the states for these characters. Using examples from echinoderms, we discuss the evolutionary transitions that have occurred in the type of morphogenesis, developmental habitat, and mode of nutrition during development. We evaluate the functional requirements associated with these transitions to infer the likelihood (frequency or rapidity) of change in a given character and of biases in the polarity of character state transitions. Using comparisons of closely related species, we evaluate the change between states in one character for dependence on the state of, or correlated changes in, other characters. Based on our analysis of congeneric species that differ in developmental habitat, we conclude that the transition between pelagic and benthic development is an ecological change that is independent of changes in morphogenesis and should be reversible. In contrast, the transition from feeding to nonfeeding development has been considered to be irreversible because it involves marked changes in larval morphology. We re-examine the transition between different modes of larval nutrition in light of recent studies that show that there exists a continuum of nutritional strategies between planktotrophy and lecithotrophy. This continuum is largely determined by variation in maternal investment and does not involve alterations in larval morphology. We suggest that the boundary between planktotrophy and lecithotrophy is frequently crossed and that this transition is reversible. Ecological changes represent the crossing of a functional threshold. Only after crossing the threshold, do larvae experience qualitatively different selective pressures that can lead to subsequent changes in morphology and development. Two different changes have occurred in the type of morphogenesis: the simplification of larval morphology that is associated with obligate (nonfeeding) lecithotrophy and the loss of the larval body plan in the evolution from indirect to direct development. It is the modification of morphology independent of the ecological changes that requires alterations in developmental processes, constrains evolutionary options, imposes irreversibility, and establishes the discrete nature of larval patterns in marine invertebrates.     

The interaction between developmental bias and natural selection: from centipede segments to a general hypothesis

Do limitations to the ways in which mutations can alter developmental processes help to determine the direction of phenotypic evolution? In the early days of neo-Darwinism, the answer given to this question was an emphatic 'no'. However, recent work, both theoretical and empirical, argues that the answer should at least be 'sometimes', and possibly even a straightforward 'yes'. Here, I examine the key concept of developmental bias, which encompasses both developmental constraint and developmental drive. I review the case of centipede segment number, which is a particularly clear example of developmental bias, but also a rather unusual one. I then consider how, in general terms, developmental bias and natural selection might interact, with the result that it is their interaction, rather than either process on its own, that determines evolutionary direction. Essentially, the whole argument is about the extent to which phenotypic variation is developmentally structured as opposed to amorphous or random. This issue can be traced back to the very beginning of evolutionary biology, and in particular to a difference of opinion between Darwin and Wallace, who emphasized, respectively, character correlation and character independence.