The effects of topological inaccuracy in evolutionary trees on the phylogenetic comparative method of independent contrasts

Computer simulations were used to test the effect of increasing phylogenetic topological inaccuracy on the results obtained from correlation tests of independent contrasts. Predictably, increasing the number of disruptions in the tree increases the likelihood of significant error in the r values produced and in the statistical conclusions drawn from the analysis. However, the position of the disruption in the tree is important: Disruptions closer to the tips of the tree have a greater effect than do disruptions that are close to the root of the tree. Independent contrasts derived from inaccurate topologies are more likely to lead to erroneous conclusions when there is a true significant relationship between the variables being tested (i.e., they tend to be conservative). The results also suggest that random phylogenies perform no better than nonphylogenetic analyses and, under certain conditions, may perform even worse than analyses using raw species data. Therefore, the use of random phylogenies is not beneficial in the absence of knowledge of the true phylogeny.

Sexual size dimorphism and reproductive investment by female spiders: A comparative analysis

We investigate the association between female reproductive investment, absolute size, and sexual size dimorphism in spiders to test the predictions of the fecundity-advantage hypothesis. The relationships between absolute size and sexual size dimorphism and aspects of female reproductive output are examined in comparative analyses using phylogenetically independent contrasts. We provide support for the idea that allometry for sexual dimorphism is the result of variation in female size more so than male size. Regression analyses suggest selection for increased fecundity in females. We argue that fecundity selection provides the only general explanation for the evolution of sexual size dimorphism in spiders.

Hibernation and non-shivering thermogenesis in the Hottentot golden mole (Amblysomus hottentottus longiceps)

Although heterothermy (hibernation and torpor) is a common feature among mammals, there is debate over whether it is a derived or ancestral trait relative to endothermic homeothermy. Determination of the physiological characteristics of primitive mammals is central to understanding the evolution of endothermy. Moreover, evaluation of physiological mechanisms responsible for endothermic heat production [e.g. non-shivering thermogenesis (NST)] is key to understanding how early mammals responded to historical climate changes and colonised different geographical regions. Here we investigated the capacity for NST and heterothermy in the Hottentot golden mole, a basal eutherian mammal. NST was measured as the metabolic response to injections of noradrenalin and heterothermy by recording body temperature in free-ranging animals. We found that hibernation and torpor occurred and that the seasonal phenotypic adjustment of NST capacity was similar to that found in other placental mammals. Using phylogenetically independent contrasts, we compared measured values of NST with those obtained from the literature. This showed that all variation in NST was accounted for by differences in phylogeny and not zoogeography. These findings lend support to the observation that NST and heterothermy occur in the Afrotheria, the basal placental mammalian clade. Furthermore, this work suggests that heterothermy, rather than homeothermy is a plesiomorphic trait in mammals and supports the notion that NST mechanisms are phylogenetically ancient.

Estimation des corrélations phylogénétiques entre paramètres d'évolution moléculaire et Traits d'histoire de vie

Depuis quelques années, l'évolution moléculaire cherche à caractériser les variations et l'intensité de la sélection grâce au rapport entre taux de substitution synonyme et taux de substitution non-synonyme (dN/dS). Cette mesure, dN/dS, a permis d'étudier l'histoire de la variation de l'intensité de la sélection au cours du temps ou de détecter des épisodes de la sélection positive. Les liens entre sélection et variation de taille efficace interfèrent cependant dans ces mesures. Les méthodes comparatives, quant a elle, permettent de mesurer les corrélations entre caractères quantitatifs le long d'une phylogénie. Elles sont également utilisées pour tester des hypothèses sur l'évolution corrélée des traits d'histoire de vie, mais pour être employées pour étudier les corrélations entre traits d'histoire de vie, masse, taux de substitution ou dN/dS. Nous proposons ici une approche combinant une méthode comparative basée sur le principe des contrastes indépendants et un modèle d'évolution moléculaire, dans un cadre probabiliste Bayésien. Intégrant, le long d'une phylogénie, sur les reconstructions ancestrales des traits et et de dN/dS nous estimons les covariances entre traits ainsi qu'entre traits et paramètres du modèle d'évolution moléculaire. Un modèle hiérarchique, a été implémenté dans le cadre du logiciel coevol, publié au cours de cette maitrise. Ce modèle permet l'analyse simultané de plusieurs gènes sans perdre la puissance donnée par l'ensemble de séquences. Un travail deparallélisation des calculs donne la liberté d'augmenter la taille du modèle jusqu'à l'échelle du génome. Nous étudions ici les placentaires, pour lesquels beaucoup de génomes complets et de mesures phénotypiques sont disponibles. À la lumière des théories sur les traits d'histoire de vie, notre méthode devrait permettre de caractériser l'implication de groupes de gènes dans les processus biologique liés aux phénotypes étudiés.

Phylogeny and metabolic scaling in mammals

The scaling of metabolic rates to body size is widely considered to be of great biological and ecological importance, and much attention has been devoted to determining its theoretical and empirical value. Most debate centers on whether the underlying power law describing metabolic rates is 2/3 (as predicted by scaling of surface area/volume relationships) or 3/4 ("Kleiber's law"). Although recent evidence suggests that empirically derived exponents vary among clades with radically different metabolic strategies, such as ectotherms and endotherms, models, such as the metabolic theory of ecology, depend on the assumption that there is at least a predominant, if not universal, metabolic scaling exponent. Most analyses claimed to support the predictions of general models, however, failed to control for phylogeny. We used phylogenetic generalized least-squares models to estimate allometric slopes for both basal metabolic rate (BMR) and field metabolic rate (FMR) in mammals. Metabolic rate scaling conformed to no single theoretical prediction, but varied significantly among phylogenetic lineages. In some lineages we found a 3/4 exponent, in others a 2/3 exponent, and in yet others exponents differed significantly from both theoretical values. Analysis of the phylogenetic signal in the data indicated that the assumptions of neither species-level analysis nor independent contrasts were met. Analyses that assumed no phylogenetic signal in the data (species-level analysis) or a strong phylogenetic signal (independent contrasts), therefore, returned estimates of allometric slopes that were erroneous in 30% and 50% of cases, respectively. Hence, quantitative estimation of the phylogenetic signal is essential for determining scaling exponents. The lack of evidence for a predominant scaling exponent in these analyses suggests that general models of metabolic scaling, and macro-ecological theories that depend on them, have little explanatory power.

Contrasting phylogenetic signals and evolutionary rates in floral traits of Neotropical lianas

The diversity of floral forms has long been considered a prime example of radiation through natural selection. However, little is still known about the evolution of floral traits, a critical piece of evidence for the understanding of the processes that may have driven flower evolution. We studied the pattern of evolution of quantitative floral traits in a group of Neotropical lianas (Bignonieae, Bignoniaceae) and used a time-calibrated phylogeny as basis to: (1) test for phylogenetic signal in 16 continuous floral traits; (2) evaluate the rate of evolution in those traits; and (3) reconstruct the ancestral state of the individual traits. Variation in floral traits among extant species of Bignonieae was highly explained by their phylogenetic history. However, opposite signals were found in floral traits associated with the attraction of pollinators (calyx and corolla) and pollen transfer (androecium and gynoecium), suggesting a differential role of selection in different floral whorls. Phylogenetic independent contrasts indicate that traits evolved at different rates, whereas ancestral character state reconstructions indicate that the ancestral size of most flower traits was larger than the mean observed sizes of the same traits in extant species. The implications of these patterns for the reproductive biology of Bignonieae are discussed. (C) 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102, 378-390.

The evolution of jumping performance in anurans: morphological correlates and ecological implications

We investigated the evolution of anuran locomotor performance and its morphological correlates as a function of habitat use and lifestyles. We reanalysed a subset of the data reported by Zug (Smithson. Contrib. Zool. 1978; 276: 1-31) employing phylogenetically explicit statistical methods (n = 56 species), and assembled morphological data on the ratio between hind-limb length and snout-vent length (SVL) from the literature and museum specimens for a large subgroup of the species from the original paper (n = 43 species). Analyses using independent contrasts revealed that classifying anurans into terrestrial, semi-aquatic, and arboreal categories cannot distinguish between the effects of phylogeny and ecological diversification in anuran locomotor performance. However, a more refined classification subdividing terrestrial species into `fossorials` and `non-fossorials`, and arboreal species into `open canopy`, `low canopy` and `high canopy`, suggests that part of the variation in locomotor performance and in hind-limb morphology can be attributed to ecological diversification. In particular, fossorial species had significantly lower jumping performances and shorter hind limbs than other species after controlling for SVL, illustrating how the trade-off between burrowing efficiency and jumping performance has resulted in morphological specialization in this group.

Ecological correlates of the threat of extinction in neotropical bird species

Predicting the threat of extinction aids efficient distribution of conservation resources. This paper utilises a comparative macroecological approach to investigate the threat of extinction in Neotropical birds. Data on ecological variables for 1708 species are analysed using stepwise regression to produce minimum adequate models, first using raw species values and then using independent contrasts (to control for phylogenetic effects). The models differ, suggesting phylogeny has significant effects. The raw species analysis reveals that number of zoogeographical regions occupied, elevational range and utilisation of specialised microhabitats were negatively associated with threat, while minimum elevation and body mass were positively associated, whereas the independent contrasts analysis only identifies zoogeographical regions as important. Confining the analysis to the 582 species restricted to a single zoogeographical region reveals elevational range and number of habitats occupied to be negatively correlated with threat whether the analysis is based on the raw data or on independent contrasts. Analysis of four contrasting zoogeographical regions highlights regional variation in the models. In two Andean regions the threat of extinction declines as the elevation range across which the species occurs increases. In the presence of substantial human populations on high Andean plateaus, a species with a greater elevational range may be more likely to persist at some (relatively) unsettled altitudes. In Central South America, the strongest predictor of threat is minimum elevation of occurrence: species with a lower minimum are less threatened. The minimum elevation result suggests that lowland species experiencing an ecological limit to their minimum elevation (min. elevation >0 m) may be more at risk than those not experiencing such a limit (min. elevation = 0 m). Finally, in southern Amazonia, where there is little altitudinal variation, the only weak predictors of threat are body size, larger species being more threatened, and number of habitats, species occupying more habitats being less threatened. These contrasting results emphasise the importance of undertaking extinction risk analyses at an appropriate geographical scale. Since the models explained only a low percentage of total variance in the data, the effects of human-mediated habitat disturbance across a wide range of habitats may be important.

Life histories of the Insectivora : the role of phylogeny, metabolism and sex differences

Life-history data for 63 species from the mammalian order Insectivora have been collated from the literature. These data were analysed for covariation and for correlations with body mass, brain mass and mass-specific resting metabolic rate. An independent contrasts method has been used to remove the effect of phylogeny. Due to uncertainties surrounding their evolutionary relationships, 22 different phylogenies of insectivores have been used as a basis for comparative analysis. The results show that several key correlations between life-history variables are only significant when certain phylogenies are used, highlighting the problems of such analyses when the phylogeny used is inaccurate. After removing the effect of phylogeny, relatively few significant correlations remain. Insectivores that have a high body mass have relatively lower metabolic rates, longer lifespans and longer gestation lengths. There is some support for a fast±slow continuum in insectivore life-history evolution: there are some significant positive correlations between measures of growth rates (e.g. gestation length and age at weaning) and lifespan, and some negative correlations between growth rates and measures of reproductive output. It is suggested that the seasonality of life of many insectivores may have played an influential role in the evolution of the group, in particular in delaying the onset of sexual maturity. There is little indication that brain size influences life-history evolution in this order, but metabolism may play an important role. The energetic requirements of maintaining high metabolic rates in small mammals such as insectivores may be constraining life histories to a greater extent than occurs in larger mammals. This effect may have obscured the relationship between metabolic rate and life histories in wider inter-order analyses. Finally, there is considerable evidence that sex differences play a large role in shaping insectivore evolution, and it is suggested that this factor must be considered more often in future studies of mammalian life histories in general.

Phylogeny and life histories of the 'Insectivora': controversies and consequences

The evolutionary relationships of the eutherian order Insectivora (Lipotyphla sensu stricto) are the subject of considerable debate. The difficulties in establishing insectivore phylogeny stem from their lack of many shared derived characteristics. The grouping is therefore something of a ‘wastebasket ’ taxon. Most of the older estimates of phylogeny, based on morphological evidence, assumed insectivore monophyly. More recently, molecular phylogenies argue strongly against monophyly, although they differ in the extent of polyphyly inferred for the order. I review the history of insectivore phylogenetics and systematics, focussing on the relationships between the six extant families (Erinaceidae – hedgehogs and moonrats, Talpidae – moles and desmans, Soricidae – shrews, Solenodontidae – solenodons, Tenrecidae – tenrecs and otter-shrews and Chrysochloridae – golden moles). I then examine how these various phylogenetic hypotheses influence the results of comparative analyses and our interpretation of insectivore life-history evolution. I assess which particular controversies have the greatest effect on results, and discuss the implications for comparative analyses where the phylogeny is controversial. I also explore and suggest explanations for certain insectivore life-history trends : increased gestation length and litter size in tenrecs, increased encephalization in moles, and the mixed fast and slow life-history strategies in solenodons. Finally, I consider the implications for comparative analyses of the recent strongly supported phylogenetic hypothesis of an endemic African clade of mammals that includes the insectivore families of tenrecs and golden moles.

Phylogeny affects estimation of metabolic scaling in mammals

The relationship between body size and metabolic rate is a crucial issue in organismal biology and evolution. There has been considerable debate over whether the scaling exponent of the relationship is 0.75 (Kleiber’s Law) or 0.67. Here we show that determination of this exponent for mammals depends on both the evolutionary tree and the regression model used in the comparative analysis. For example, more recent molecular-based phylogenies tend to support a 0.67 exponent, whereas older phylogenies, mostly based on morphological data, suggest a 0.75 exponent. However, molecular phylogenies yield more variable results than morphological phylogenies and thus are not currently helping to resolve the issue.

Determinants of local abundance in a major radiation of Australian passerines (Aves: Meliphagoidea)

Aim  To identify the factors that contribute to variation in abundance (population density), and to investigate whether habitat breadth and diet breadth predict macroecological patterns in a suborder of passerine birds (Meliphagoidea).
Location  Australia (including Tasmania).
Methods  Mean abundance data were collated from site surveys of bird abundance (the Australian Bird Count); range size and latitudinal position data from published distribution maps; and body mass and diet breadth information from published accounts. A diversity index of habitats used (habitat breadth) was calculated from the bird census data. We used bivariate correlation and multiple regression techniques, employing two phylogenetic comparative methods: phylogenetic generalized least squares and independent contrasts.

Results  Body mass and latitude were the only strong predictors of abundance, with larger-bodied and lower-latitude species existing at lower densities. Together, however, body mass and latitude explained only 11.1% of the variation in mean abundance. Range size and habitat breadth were positively correlated, as were diet breadth and body mass. However, neither range size, nor habitat breadth and diet breadth, explained patterns in abundance either directly or indirectly.
Main conclusions  Levels of abundance (population density) in meliphagoid birds are most closely linked to body mass and latitudinal position, but not range size. As with many other macroecological analyses, we find little evidence for aspects of niche breadth having an effect on patterns of abundance. We hypothesize that evolutionary age may also have a determining effect on why species tend to be rarer (less abundant) in the tropics.

Basal metabolic rate of canidae from hot deserts to cold arctic climates

Canids form the most widely distributed family within the order Carnivora, with members present in a multitude of different environments from cold arctic to hot, dry deserts. We reviewed the literature and compared 24 data sets available on the basal metabolic rate (BMR) of 12 canid species, accounting for body mass and climate, to examine inter- and intraspecific variations in mass-adjusted BMR between 2 extreme climates (arctic and hot desert). Using both conventional and phylogenetically independent analysis of covariance, we found that canids from the arctic climate zone had significantly higher mass-adjusted BMR than species from hot deserts. Canids not associated with either arctic or desert climates had an intermediate and more variable mass-adjusted BMR. The climate effect also was significant at the intraspecific level in species for which we had data in 2 different climates. Arctic and desert climates represent contrasting combinations of ambient temperatures and water accessibility that require opposite physiological adaptations in terms of metabolism. The fact that BMR varies within species when individuals are subjected to different climate regimes further suggests that climate is an important determinant of BMR.

The evolution of jumping performance in anurans: morphological correlates and ecological implications

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Diversity and evolution of macrohabitat use, body size and morphology in a monophyletic group of Neotropical pitvipers (Bothrops)

The Neotropical pitviper genus Bothrops comprises about 40 species, which occur in all main ecosystems of cis-Andean South America. We explored the relationships of body size and form (tail length and stoutness) with macrohabitat use in 20 forms of Bothrops. Sen-ii-arboreal habits appeared only in forest forms. Semi-arboreals are significantly more slender and have longer tails than terrestrials; body size is not significantly different between terrestrials and semi-arboreals. Within Bothrops, independent contrasts for macrohabitat use were significantly correlated with contrasts of tail size (positively) and stoutness (negatively); thus, the more arboreal the species, the longer its tail and the more slender its body. Contrasts of adult body size seems to remain constant over the lower range of macrohabitat use, but to decrease in species of Bothrops which are more arboreal. Reconstructions of character states indicate that: (1) the ancestor of Bothrops was a small, stout, terrestrial species; (2) semi-arboreal habits appeared one to three times in the genus; (3) a decrease in stoutness and an increase in tail length occurred along with an increase in arboreality in some clades. Although macrohabitat use seems to be important in determining body form in Bothrops, our results also indicate that tail size, stoutness and body size may also be affected by selective agents other than macrohabitat use. The selective agents responsible for the shifts in macrohabitat use in Bothrops are still uncertain, although they may have included prey availability and/or predation pressure. The plasticity of macrohabitat use, morphology and body size described in this study may have been key features that facilitated the highly successful ecological diversification of Bothrops in South America.