Why Not to Do Two-Species Comparative Studies: Limitations on Inferring Adaptation

Claims about adaptation are commonly made from comparative studies involving only two species (or only two populations of a single species). Our main purpose here is to alert practitioners to several logical and statistical problems associated with using two-species comparisons for studying adaptation and to outline some alternative approaches. Multispecies comparisons are one such alternative. However, data from multiple species may not be independent or identically distributed in the statistical sense, which violates assumptions of ordinary statistical methods (Harvey and Pagel 1991). We therefore also discuss one phylogenetically based statistical method that can be employed for valid hypothesis testing with comparative data, Felsenstein’s (1985) method of phylogenetically independent contrasts. We discuss briefly how such methods can be employed, even with incomplete phylogenetic information, and also how data for multiple populations within species can enhance comparative analyses. Phylogenetically based analyses come in a variety of flavors, and our penultimate section discusses some differences in perspectives regarding statistical hypothesis testing in a phylogenetic context. We conclude by pointing out that many of our criticisms of two-species comparisons apply also to comparisons aimed at discovering mechanisms underlying physiological differences between species

Relationships of Basal Metabolism and Life History Attributes in Neotomine-Peromyscine Rodents (Cricetidae: Neotominae).

With the exception of a positive relationship between energy expenditure and number of offspring per litter, few links have been made between energy expenditure and life history attributes in mammals. The purpose of this study was to examine relationships between basal metabolic rate (BMR) and life history attributes among 26 species within the Neotomine–Peromyscine rodents. Specifically, I used independent contrasts to determine whether variation in BMR is related to variation in life history attributes that represent reproductive effort and maturation, and I determined if there is an offspring size versus offspring number trade-off. My results demonstrate that within the Neotomine–Peromyscine rodents, 1) there exists an offspring number versus offspring size trade-off whereby taxa that have a large residual number of offspring per litter have a small residual neonate mass, 2) BMR is related to this trade-off whereby taxa that have large residual BMR have small residual neonate mass and a trend towards a large number of offspring per litter, and 3) BMR is not related to total reproductive effort as represented by total litter mass, total weanling mass, or total growth rate of the litter from birth to weaning. My results suggest that high BMR facilitates a large number of small offspring per reproductive event. A large number of small offspring may confer a fitness advantage for taxa with compensatory growth mechanisms for weaned young that minimize fecundity trade-offs with small offspring size

Host body size and the diversity of tick assemblages on Neotropical vertebrates

AbstractIdentifying the factors that influence the species diversity and distribution of ticks (Acari: Ixodida) across vertebrate host taxa is of fundamental ecological and medical importance. Host body size is considered one of the most important determinants of tick abundance, with larger hosts having higher tick burdens. The species diversity of tick assemblages should also be greater on larger-bodied host species, but empirical studies testing this hypothesis are lacking. Here, we evaluate this relationship using a comparative dataset of feeding associations from Panama between 45 tick species and 171 host species that range in body size by three orders of magnitude. We found that tick species diversity increased with host body size for adult ticks but not for immature ticks. We also found that closely related host species tended to have similar tick species diversity, but correcting for host phylogeny did not alter the relationships between host body size and tick species diversity. The distribution of tick species was highly aggregated, with approximately 20% of the host species harboring 80% of all tick species, following the Pareto principle or 20/80 Rule. Thus, the aggregated pattern commonly observed for tick burdens and disease transmission also holds for patterns of tick species richness. Our finding that the adult ticks in this system preferentially parasitize large-bodied host species suggests that the ongoing anthropogenic loss of large-bodied vertebrates is likely to result in host-tick coextinction events, even when immature stages feed opportunistically. As parasites play critical roles in ecological and evolutionary processes, such losses may profoundly affect ecosystem functioning and services

Are substitution rates and RNA editing correlated?

<p>Abstract</p> <p>Background</p> <p>RNA editing is a post-transcriptional process that, in seed plants, involves a cytosine to uracil change in messenger RNA, causing the translated protein to differ from that predicted by the DNA sequence. RNA editing occurs extensively in plant mitochondria, but large differences in editing frequencies are found in some groups. The underlying processes responsible for the distribution of edited sites are largely unknown, but gene function, substitution rate, and gene conversion have been proposed to influence editing frequencies.</p> <p>Results</p> <p>We studied five mitochondrial genes in the monocot order Alismatales, all showing marked differences in editing frequencies among taxa. A general tendency to lose edited sites was observed in all taxa, but this tendency was particularly strong in two clades, with most of the edited sites lost in parallel in two different areas of the phylogeny. This pattern is observed in at least four of the five genes analyzed. Except in the groups that show an unusually low editing frequency, the rate of C-to-T changes in edited sites was not significantly higher that in non-edited 3^rdcodon positions. This may indicate that selection is not actively removing edited sites in nine of the 12 families of the core Alismatales. In all genes but <it>ccm</it>B, a significant correlation was found between frequency of change in edited sites and synonymous substitution rate. In general, taxa with higher substitution rates tend to have fewer edited sites, as indicated by the phylogenetically independent correlation analyses. The elimination of edited sites in groups that lack or have reduced levels of editing could be a result of gene conversion involving a cDNA copy (retroprocessing). If so, this phenomenon could be relatively common in the Alismatales, and may have affected some groups recurrently. Indirect evidence of retroprocessing without a necessary correlation with substitution rate was found mostly in families Alismataceae and Hydrocharitaceae (e.g., groups that suffered a rapid elimination of all their edited sites, without a change in substitution rate).</p> <p>Conclusions</p> <p>The effects of substitution rate, selection, and/or gene conversion on the dynamics of edited sites in plant mitochondria remain poorly understood. Although we found an inverse correlation between substitution rate and editing frequency, this correlation is partially obscured by gene retroprocessing in lineages that have lost most of their edited sites. The presence of processed paralogs in plant mitochondria deserves further study, since most evidence of their occurrence is circumstantial.</p

Evidence of fruit syndromes in the recently diverged wild tomato clade opens new possibilities for the study of fleshy fruit evolution

Societal Impact Statement Fleshy fruits provide humans with many flavorful and nutritious crops. Understanding the diversity of these plants is fundamental to managing agriculture and food security in a changing world. This study surveyed fruit trait variation across species of tomato wild relatives and explored associations among color, size, shape, sugars, and acids. These wild tomato species native to South America can be interbred with the economically important cultivated tomato. Beyond its application to tomatoes, deepening our knowledge of how fruit traits evolve together is valuable to crop improvement efforts aimed at breeding more nutritious and appealing varieties of fruits. Summary Fleshy fruits display a striking diversity of traits, many of which are important for agriculture. The evolutionary drivers of this variation are not well understood, and most studies have relied on variation found in the wild. Few studies have explored this question on a fine-grained scale with a group of recently diverged species while controlling for environmental effects. We developed the tomato clade as a novel system for fruit trait evolution research by presenting the first common garden-based systematic survey of variation and phylogenetic signal in color, nutrition, and morphology traits across all 13 species of tomato wild relatives (Solanum sect. Lycopersicon). We laid the groundwork for further testing of potential evolutionary drivers by assessing patterns of clustering and correlation among disperser-relevant fruit traits as well as historical climate variables. We found evidence of two distinct clusters of associated fruit traits defined by color, sugar type, and malic acid concentration. We also observed correlations between a fruit\u27s external appearance and internal nutrient content that could function as honest signals to dispersers. Analyses of historical climate and soil variables revealed an association between red/orange/yellow fruits and high annual average temperature. Our results establish the tomato clade as a promising system for testing hypotheses on the drivers of divergence behind early-stage fleshy fruit evolution, particularly selective pressure from frugivores

The evolution of human diversity: a phylogenetic approach

The socio-ecological correlates of cross-cultural variation in lactase persistence, sexual dimorphism in stature, and wealth inheritance in Africa were investigated, using phylogenetic comparative methods to control for the non-independence of populations (Galton's problem). Felsenstein's method of comparative analysis using independent contrasts, and Pagel's phylogenetic maximum likelihood model, were used. Genetic and linguistic trees were used as models of the past relationships among populations. Lactase persistence was found to be associated with pastoralism but not with solar intensity or aridity. This is consistent with the hypothesis that high lactose digestion capacity in adults is an adaptation to dairying. This result does not support the hypotheses that low solar radiation at high latitudes and aridity are additional selective pressures for lactase persistence. Cross-cultural variation in stature was associated with women's work. Women are taller, relative to men, in societies where women contribute more to subsistence. In Africa, patrilineal wealth inheritance is associated with pastoralism and polygyny. Patrilineal wealth inheritance is adaptive if inherited wealth benefits sons more than daughters, which is probably the case in both polygynous and pastoralist societies. It is hypothesised that matrilineal inheritance arises from wealth inheritance to daughters. Inheritance to daughters is adaptive if the additional benefits of wealth inheritance to sons do not outweigh the risk of paternity uncertainty of sons' offspring. The transmission, between populations, of those bio-cultural traits in the comparative analyses was also investigated. The association between each trait in a population, and that trait in the population's phylogenetic sister-group and nearest geographical neighbour(s) were compared using regression. The majority of traits were found to be associated with phylogeny. Some traits showed an additional association with geographical neighbours. Vertical transmission, from `mother' to `daughter' populations, appears to be more important than geographical diffusion between neighbouring populations, for the majority of the traits tested here

Mating evolution in Gambusia (Poeciliidae) : an integration of behavior, molecules and morphology

textFemale mate choice and male courtship display are critical behaviors for the understanding of character evolution driven by sexual selection. This thesis is designated to understand the evolutionary mechanism of these two behaviors with mosquito fish (Gambusia). In the first chapter, collaborated with Dr. Mark Kirkpatrick, we demonstrated positive coevolution of courtship display and morphological signatures of male coercion and male advantage in sexually antagonistic adaptation across 10 Gambusia species. This finding suggested that male display may have caused the evolution of morphologies involved in SAC, or conversely it may have evolved as a palliative byproduct of the morphologies. This unexpected observation raised new interpretation about evolutionary cause and consequence of displays across different mating systems. The second chapter examined whether neuromolecular underpinning of G. affinis female mate choice is canalized or plastic in mating systems that show variable extant of mate choice. With Dr. Mary Ramsey, we should positive correlations between gene expression and female preference strength during exposure to courting heterospecific males, but a reversed pattern following exposure to coercive heterospecific males. This suggested that the neuromolecular entities associated with female preference are plastic and responsive to different male phenotypes (courting or coercive) rather than a canalized response linked to mating system. Further, I proposed that female behavioral plasticity may involve learning because female association patterns shifted with experience/age. Compared to younger females, I find that more experienced females spend less time near coercive males but associate more with males in the presence of courters. We thus suggested a conserved learning-based neuromolecular process underlying the diversity of female mate preference across the mate choice and coercion-driven mating systems.Ecology, Evolution and Behavio