Adaptation, Phylogenetic Inertia, and the Method of Controlled Comparisons

Phylogenetic inertia and Darwin’s higher law

Phylogenetic inertia is a difficult issue in evolutionary biology because we have yet to reach a consensus about how to measure it. In this study a comparative approach is used to evaluate phylogenetic inertia in 14 demographic and morphological characters in 10 species and one subspecies of the genus Tithonia (Asteraceae). Three different methods, autocorrelational analysis, phylogenetic correlograms, and ancestor-state reconstruction, were used to evaluate phylogenetic inertia in these traits. Results were highly dependent on the method applied. Autoregression and phylogenetic eigenvector regression (PVR) methods found more inertia in morphological traits. In contrast, phylogenetic correlograms and ancestor-state reconstruction suggest that morphological characters exhibit less phylogenetic inertia than demographic ones. The differences between results are discussed and methods are compared in an effort to understand phylogenetic inertia more thoroughly.

[Socio-ecological theories predict that females adapt their social behaviour to their environment. On the other hand, as a result of phylogenetic inertia, social behaviour may be slow to catch up when the environment changes. If social behaviour is adapted to the environment, competition and co-operation among females is predicted to reflect the characteristics of food sources. Contest competition both between and within groups is expected to result in alliances among related, philopatric, females. We compared social relationships and food characteristics of two sympatric and congeneric primate species, the red colobus and the black-and-white colobus of the Tai National Park, Ivory Coast. We found that affiliative interactions among females were comparable between the species. The differences in food characteristics could explain why black-and-white females competed more often than did red colobus females, both at the intra- and inter-group level. In contrast to socio-ecological theory, female inter-group aggression was not linked to female philopatry in black-and-white colobus. The species differed from each other and from other populations of the same or closely related species with respect to their inter-group behaviour which indicates that phylogenetic inertia did not constrain this aspect of social behaviour., Socio-ecological theories predict that females adapt their social behaviour to their environment. On the other hand, as a result of phylogenetic inertia, social behaviour may be slow to catch up when the environment changes. If social behaviour is adapted to the environment, competition and co-operation among females is predicted to reflect the characteristics of food sources. Contest competition both between and within groups is expected to result in alliances among related, philopatric, females. We compared social relationships and food characteristics of two sympatric and congeneric primate species, the red colobus and the black-and-white colobus of the Tai National Park, Ivory Coast. We found that affiliative interactions among females were comparable between the species. The differences in food characteristics could explain why black-and-white females competed more often than did red colobus females, both at the intra- and inter-group level. In contrast to socio-ecological theory, female inter-group aggression was not linked to female philopatry in black-and-white colobus. The species differed from each other and from other populations of the same or closely related species with respect to their inter-group behaviour which indicates that phylogenetic inertia did not constrain this aspect of social behaviour.]

A number of philosophers and ‘evolutionary psychologists’ have argued that attacks on adaptationism in contemporary biology are misguided. These thinkers identify anti-adaptationism with advocacy of non-adaptive modes of explanation. They overlook the influence of anti-adaptationism in the development of more rigorous forms of adaptive explanation. Many biologists who reject adaptationism do not reject Darwinism. Instead, they have pioneered the contemporary historical turn in the study of adaptation. One real issue which remains unresolved amongst these methodological advances is the nature of ‘phylogenetic inertia’. To what extent is an adaptive explanation needed for the persistence of a trait as well as its origin?.

The determination of whether the pattern of trait evolution observed in a comparative analysis of species data is due to adaptation to current environments, to phylogenetic inertia, or to both of these forces requires that one control for the effects of either force when making an assessment of the evolutionary role of the other. Orzack and Sober (2001) developed the method of controlled comparisons to make such assessments; their implementation of the method focussed on a discretely varying trait. Here, we show that the method of controlled comparisons can be viewed as a meta-method, which can be implemented in many ways. We discuss which recent methods for the comparative analysis of continuously distributed traits can generate controlled comparisons and can thereby be used to properly assess whether current adaptation and/or phylogenetic inertia have influenced a trait's evolution. The implementation of controlled comparisons is illustrated by an analysis of sex-ratio data for fig wasps. This analysis suggests that current adaptation and phylogenetic inertia influence this trait.

On the relationship between mitochondrion and longevity in mammals, two viewpoints have been proposed: one found that the amino acid substitution rates of most of the mitochondrial DNA-coding peptides were positively correlated with longevity, while the other raised the opposite view. To resolve this dichotomy, and to explore the relationship between mtDNA evolution and longevity in mammals, we examined this relationship in 85 mammal species, at the nucleotide sequence level. Previous studies have demonstrated that phylogenetic inertia, substitution saturation, and body mass can affect the relationship between longevity and substitution rate. Therefore, analyses should take these factors into account. This study found that after controlling the aforementioned factors, no significant positive or negative relationship existed between mitochondrial DNA evolutionary rate and longevity except for CYTB, partly agreeing with a previous study. Variations of longevity can be explained partly by the evolutionary rate of CYTB, but other influencing factors still need to be studied in the future.

fenses. We evaluated the association between herbivory and the amount of azoxyglycosides in the Cycadales using phylogenetic independent contrasts. We hypothesized that herbivory types should be related to the presence of macrozamin and cycasin, thus herbivory should be lower in species with higher concentrations of azoxyglycosides. We gathered information available on the literature of these two characters as well as life form, geographic distribution, height, and seed volume for the majority of cycad species, in order to assess correlated evolution and control for possible allometric effects. Herbivory types and macrozamin were negatively correlated, suggesting a possible defensive function for macrozamin against herbivores. No significant correlation was observed between cycasin percent and herbivory type. However, when analysed using phylogenetic independent contrasts and thus removing the historical effect, the association did not hold. This suggests that the presence of metabolites in plants may have evolved for some other reason, and has been mantained among cycads perhaps by phylogenetic inertia. The presence of macrozamin should then be explained as an exaptation, playing today an important role in defense against herbivores. Furthermore, this analysis showed that macrozamin has independently and repeatedly (Bowenia, Macrozamia, Stangeria) increased over evolutionary time.

Microevolutionary studies often find that complex quantitative characters are highly evolvable and adapted to the local environment, while macroevolutionary studies often show evidence of strong phylogenetic effects and stasis. In this contribution, we show how phylogenetic comparative methods can be used to test hypotheses that may help resolve this paradox. As a test case, we studied the interplay between adaptation and phylogenetic inertia on the thermobiology of 32 species of Liolaemus (Squamata: Liolaemidae), a genus of South American lizards living under diverse climatic conditions. Despite a strong phylogenetic effect in the preferred (selected) body temperature, we found clear evidence that this variable is adapted to local temperature and climate. After controlling for adaptation to the thermal environment, little influence of phylogeny was left. This indicates that the phylogenetic effect was not caused by a lag or slowness in adaptation but primarily by the distribution of the thermal environments on the phylogeny. This can be due to thermal niche tracking. In contrast, we found little or no evidence for adaptation to the thermal environment in either cooling or heating rates, critical thermal minimum, or body size.

The same anthocyanins served four different ways: Insights into anthocyanin structure-function relationships from the wintergreen orchid, Tipularia discolor

Genomic tools have transformed our understanding of species and population genetic structure in landscapes. However, discerning the impacts of neutral and adaptive evolutionary forces remains challenging, largely due to the scarcity of tools capable of measuring a broad spectrum of phenotypic traits. We used spectroscopic data from preserved leaves to test for adaptive divergence among populations of live oaks (Quercus section Virentes) across genetic and phylogenetic levels. The monophyletic lineage includes seven species that diversified under sympatric, parapatric and allopatric speciation modes. We used 427 individuals to test for isolation-by-distance (IBD) and isolation-by-environment (IBE), as well as the influences of selection and phylogenetic inertia on traits. Finally and to examine how phylogenetic signals are distributed across their foliar reflectance spectra. Partial redundancy analyses (pRDA) revealed that (IBE explains more phenotypic variation than (IBD among sympatric species, particularly in certain spectral regions and traits derived from spectra. Across the phylogeny, phylogenetic generalized least squares (PGLS) models show that environmental variables—including minimum temperature of the coldest month and annual precipitation—predict traits related to stress tolerance across climatic gradients, such as lignin content and anthocyanin levels. These results demonstrate that leaf reflectance spectra can be used to capture adaptive differentiation and evolutionary history across scales, offering a powerful, non-destructive tool for linking phenotype, environment, and evolutionary processes in long-lived plant lineages.

This chapter surveys the philosophical problems raised by the two Darwinian claims of the existence of Tree of Life and the explanatory power of natural selection. It explores the specificity of explanations by natural selection, emphasizing the high context dependency of any process of selection. Some consequences are drawn about the difficulty of those explanations to fit a nomological model of explanation, and the irreducibility of their historic‐narrative dimension. The paper introduces debates about units of selection, stating the compelling force of genic selectionism but highlighting some critiques. It then addresses the limitations of selectionist explanations: the compared status of selection, drift, and phylogenetic inertia are investigated, and the debates over adaptationism are presented, with the aim of defining the varieties of adaptationisms as research programs. In order to assess the scope of natural selection, the chapter addresses weak and strong challenges to the Synthetic theory of evolution both from paleontology (punctuated equilibria, Gould’s contingency thesis) and the evolutionary theory of development. We finally sketch some consequences of evolutionary theory concerning philosophical questions about human nature, on the basis of the hypothesis of the universality of selectionist explanations: this part deals mostly with epistemology and psychology.

The phylogeographical and systematic relationships among species in the tropical marine fish genus Dascyllus were inferred using mitochondrial DNA (mtDNA) sequence data. Although our results were generally consistent with previously published phylogenies based on both morphological and mitochondrial data, our broad taxonomic and geographical sampling design revealed novel insights into the phylogenetic history of Dascyllus that had escaped previous notice. These results include: (a) the polyphyletic nature of D. reticulatus mtDNAs, representing two divergent and geographically separated lineages, one shared with D. flavicaudus and the second forming the sister lineage of D. carneus; (b) the paraphyly of D. trimaculatus relative to the closely related D. abisella; and (c) phylogeographical structure within the widespread taxa D. aruanus and D. trimaculatus. Application of a molecular clock permits us to posit a causative role for tectonic and oceanic changes regarding some Dascyllus speciation events. Finally, we mapped body size and the presence or absence of protogynous sex change on the mtDNA tree, and tested published hypotheses regarding determinants of the evolution of mating system and protogyny in the genus. Our data rejected a model based on body size but not one based on phylogenetic inertia. The ability to change sex arose once in the ancestor to the entire genus, and was lost once in the ancestor of the D. trimaculatus complex. For taxa that are as geographically widespread as many Indo-Pacific genera, this study highlights the importance of adequate geographical sampling when inferring patterns of species diversification and life history evolution.

Bivariate scaling analyses can reveal interesting correlations between individual biological variables, but inference of actual causal links in complex networks requires multiple tests to satisfy the criterion of isolation. Mammalian brain tissue has high energy demands, so energy supply is inevitably a key issue in evolution of the primate brain, especially for large-brained hominids. Various hypotheses have proposed a direct link between brain size and metabolic turnover in adults, but the author’s Maternal Energy Hypothesis (MEH) instead focuses on energy supplied by the mother during brain development up to weaning. This hypothesis is supported by various empirical findings, but it has also been challenged, particularly on the basis that these findings do not survive tests conducted to eliminate effects of phylogenetic inertia. New comparative analyses of brain size in mammals with improved datasets have, however, confirmed links to both basal metabolic rate and gestation period, complying with core predictions of MEH. The evidence now available in support of MEH is reviewed and some implications for brain evolution are explored. A widely recognized general trend towards increase in average relative brain size during mammalian evolution has recently been challenged by a study of brain size in bats that inferred, exclusively through analysis of data from extant species, that brain size has actually undergone reduction in numerous lineages. It is shown that the statistical test used to test for directionality of evolution was inappropriate. A review of fossil evidence for brain evolution in primates, cetaceans and carnivores confirms the generally accepted trend towards increased average brain size through the Tertiary. Progressive increase in mammalian relative brain size over time is at least partially attributable to increases in the level and efficiency of maternal investment. Energetic aspects, including those invoked in the MEH, are of special importance for outstandingly large-brained mammals such as hominids.

The hands and feet of primates fulfill a variety of biological roles linked with food acquisition and positional behavior. Current explanations of shape differences in cheiridial morphology among prosimians are closely tied to body size differences. Although numerous studies have examined the relationships between body mass and limb morphology in prosimians, no scaling analysis has specifically considered hand and foot dimensions and intrinsic proportions. In this study, we present such an analysis for a sample of 270 skeletal specimens distributed over eight prosimian families. The degree of association between size and shape was assessed using nonparametric correlational techniques, while the relationship between each ray element length and body mass (from published data and a body mass surrogate) was tested for allometric scaling. Since tarsiers and strepsirrhines encompass many taxa of varying degrees of phylogenetic relatedness, effective degrees of freedom were calculated, and comparisons between families were performed to partially address the problem of statistical nonindependence and "phylogenetic inertia." Correlational analyses indicate negative allometry between relative phalangeal length (as reflected by phalangeal indices) and body mass, except for the pollex and hallux. Thus, as size increases, there is a significant decrease in the relative length of the digits when considering all prosimian taxa sampled. Regression analyses show that while the digital portion of the rays scales isometrically with body mass, the palmar/plantar portion of the rays often scales with positive allometry. Some but not all of these broadly interspecific allometric patterns remain statistically significant when effective degrees of freedom are taken into account. As is often the case in interspecific scaling, comparisons within families show different scaling trends in the cheiridia than those seen across families (i.e., lorisids, indriids, and lemurids exhibit rather different allometries). The interspecific pattern of positive allometry that appears to best characterize the metapodials of prosimians, especially those of the foot, parallels differences found in the morphology of the volar skin. Indeed, relatively longer metapodials appear to covary with flatter and more coalesced volar pads, which in turn slightly improve frictional force for animals that are at a comparative disadvantage while climbing because of their larger mass. Despite the essentially isometric relationship found between digit length and body mass across prosimians, examination of the residual variation reveals that tarsiers and Daubentonia possess, relative to their body sizes, remarkably long fingers. Such marked departures between body size and finger length observed in these particular primates are closely linked with specialized modes of prey acquisition and manipulation involving the hands.

Dunbar suggests structural, behavioral, and cognitive mechanisms to mitigate the costs of living in large groups. While we generally concur with the notion of group size effects on female productivity, we call for a more explicit treatment of how functional support alleviates social costs and disagree with the outright dismissal of ecological drivers and phylogenetic inertia.