Quantitative traits and diversification

Quantitative traits have long been hypothesized to affect speciation and extinction rates. For example, smaller body size or increased specialization may be associated with increased rates of diversification. Here, I present a phylogenetic likelihood-based method (quantitative state speciation and extinction [QuaSSE]) that can be used to test such hypotheses using extant character distributions. This approach assumes that diversification follows a birth-death process where speciation and extinction rates may vary with one or more traits that evolve under a diffusion model. Speciation and extinction rates may be arbitrary functions of the character state, allowing much flexibility in testing models of trait-dependent diversification. I test the approach using simulated phylogenies and show that a known relationship between speciation and a quantitative character could be recovered in up to 80% of the cases on large trees (500 species). Consistent with other approaches, detecting shifts in diversification due to differences in extinction rates was harder than when due to differences in speciation rates. Finally, I demonstrate the application of QuaSSE to investigate the correlation between body size and diversification in primates, concluding that clade-specific differences in diversification may be more important than size-dependent diversification in shaping the patterns of diversity within this group.     

FiSSE: A simple nonparametric test for the effects of a binary character on lineage diversification rates

It is widely assumed that phenotypic traits can influence rates of speciation and extinction, and several statistical approaches have been used to test for correlations between character states and lineage diversification. Recent work suggests that model‐based tests of state‐dependent speciation and extinction are sensitive to model inadequacy and phylogenetic pseudoreplication. We describe a simple nonparametric statistical test (“FiSSE”) to assess the effects of a binary character on lineage diversification rates. The method involves computing a test statistic that compares the distributions of branch lengths for lineages with and without a character state of interest. The value of the test statistic is compared to a null distribution generated by simulating character histories on the observed phylogeny. Our tests show that FiSSE can reliably infer trait‐dependent speciation on phylogenies of several hundred tips. The method has low power to detect trait‐dependent extinction but can infer state‐dependent differences in speciation even when net diversification rates are constant. We assemble a range of macroevolutionary scenarios that are problematic for likelihood‐based methods, and we find that FiSSE does not show similarly elevated false positive rates. We suggest that nonparametric statistical approaches, such as FiSSE, provide an important complement to formal process‐based models for trait‐dependent diversification.     

Four-cluster analysis: a simple method to test phylogenetic hypotheses

A simple statistical test for comparing three alternative phylogenetic hypotheses for four monophyletic groups is presented. This test is based on the minimum-evolution principle, and it does not require any information regarding the branching order within each monophyletic group. It is computationally efficient and can be easily extended to five or more monophyletic groups.      

Contingent predictability in evolution: key traits and diversification

Key innovations have often been invoked to explain the exceptional diversification of particular groups. However, there are few convincing examples of traits that are repeatedly and consistently associated with increased diversification. The paucity of such cases may reflect the contingent nature of the diversifying effect of key traits. These contingencies can be viewed as statistical interactions between the trait and at least three kinds of factors: (1) other taxa, (2) other traits of the group itself, and (3) the physical environment. I describe tentative examples in each of these categories: (1) a dampening of the diversification of clades with image-forming eyes by groups that earlier evolved such eyes, (2) an effect of growth form (woody or herbaceous) on the diversifying effect of biotic seed dispersal in angiosperms, and (3) an effect of atmospheric CO(2) level on the diversifying effect of C(4) photosynthesis in monocots. These examples suggest the need for more complex analyses of the relationship between possible key traits and diversification. They also suggest that radiations may be predictable given certain circumstances, thus supporting a view of evolution as both predictable and contingent. Ironically, a certain degree of predictability may be critical to arguments for evolutionary contingency.     

Shift in diversification in sister-clade comparisons: a more powerful test

Tests of shift in diversification associated with key innovations or directional environmental change can be performed with sister-clade comparisons. This approach is attractive because it does not require detailed phylogenetic information. I propose a new likelihood ratio test based on fitting two models of diversification. I show how this test differs from a previous likelihood ratio test based on the geometric distribution. With simulations from a wide range of situations, I show that the new test performs much better than this test and the traditional test by Slowinski and Guyer. The proposed test performs at least as well as the species richness contrast test that has been proposed by several authors in four versions. A power analysis with low number of pairs of sister clades showed that the new test could detect a shift in diversification with five or less pairs of sister clades, whereas the diversity contrast test cannot detect any shift in this situation. The former appears as more powerful than the latter, and therefore is recommended when the number of pairs of sister clades is low (less than 10). All other tests should not be used as the present study showed they lack statistical power and robustness.     

Relating environmental variation to selection on reaction norms: an experimental test

Theoretical models predict that selection on reaction norms should depend on the relative frequency of environmental states experienced by a population. We report a laboratory experimental test of this prediction for thermal performance curves of larval growth rate in Pieris rapae in relation to their thermal environment. We measured short-term relative growth rate (RGR) for each individual at a series of five temperatures, and then we assigned individuals randomly to warm or cool selection treatments, which differ in the frequency distributions of environmental temperatures. Selection gradient analyses of two independent experiments demonstrated significant positive selection for increasing RGR, primarily through its effects on survival to adulthood and on development rate. In both the warm and cool selection treatments, the magnitude of directional selection on RGR was consistently greater at lower (suboptimal) temperatures than at higher temperatures; differences in selection between the treatments did not match model predictions. The temporal order and duration of environmental conditions may affect patterns of selection on thermal performance curves and other continuous reaction norms, complicating the connections between variation in environment, phenotype, and fitness.     

The complete linkage disequilibrium test: a test that points to causative mutations underlying quantitative traits

Background

Genetically, SNP that are in complete linkage disequilibrium with the causative SNP cannot be distinguished from the causative SNP. The Complete Linkage Disequilibrium (CLD) test presented here tests whether a SNP is in complete LD with the causative mutation or not. The performance of the CLD test is evaluated in 1000 simulated datasets.

Methods

The CLD test consists of two steps i.e. analysis I and analysis II. Analysis I consists of an association analysis of the investigated region. The log-likelihood values from analysis I are next ranked in descending order and in analysis II the CLD test evaluates differences in log-likelihood ratios between the best and second best markers. Under the null-hypothesis distribution, the best SNP is in greater LD with the QTL than the second best, while under the alternative-CLD-hypothesis, the best SNP is alike-in-state with the QTL. To find a significance threshold, the test was also performed on data excluding the causative SNP. The 5^th, 10^th and 50^th highest T_CLD value from 1000 replicated analyses were used to control the type-I-error rate of the test at p = 0.005, p = 0.01 and p = 0.05, respectively.

Results

In a situation where the QTL explained 48% of the phenotypic variance analysis I detected a QTL in 994 replicates (p = 0.001), where 972 were positioned in the correct QTL position. When the causative SNP was excluded from the analysis, 714 replicates detected evidence of a QTL (p = 0.001). In analysis II, the CLD test confirmed 280 causative SNP from 1000 simulations (p = 0.05), i.e. power was 28%. When the effect of the QTL was reduced by doubling the error variance, the power of the test reduced relatively little to 23%. When sequence data were used, the power of the test reduced to 16%. All SNP that were confirmed by the CLD test were positioned in the correct QTL position.

Conclusions

The CLD test can provide evidence for a causative SNP, but its power may be low in situations with closely linked markers. In such situations, also functional evidence will be needed to definitely conclude whether the SNP is causative or not.     

Statistical analysis of diversification with species traits

Testing whether some species traits have a significant effect on diversification rates is central in the assessment of macroevolutionary theories. However, we still lack a powerful method to tackle this objective. I present a new method for the statistical analysis of diversification with species traits. The required data are observations of the traits on recent species, the phylogenetic tree of these species, and reconstructions of ancestral values of the traits. Several traits, either continuous or discrete, and in some cases their interactions, can be analyzed simultaneously. The parameters are estimated by the method of maximum likelihood. The statistical significance of the effects in a model can be tested with likelihood ratio tests. A simulation study showed that past random extinction events do not affect the Type I error rate of the tests, whereas statistical power is decreased, though some power is still kept if the effect of the simulated trait on speciation is strong. The use of the method is illustrated by the analysis of published data on primates. The analysis of these data showed that the apparent overall positive relationship between body mass and species diversity is actually an artifact due to a clade-specific effect. Within each clade the effect of body mass on speciation rate was in fact negative. The present method allows to take both effects (clade and body mass) into account simultaneously.     

The ParaSight-F test: a simple rapid manual dipstick test to detect Plasmodium falciparum infection

A rapid diagnostic for Plasmodium falciparum based on an antigen capture has been incorporated in a simple, easily interpreted dipstick by Becton Dickinson Advanced Diagnostics. In this article Clive Shiff, Japhet Minjas and Zul Premji discuss its evaluation in rural Tanzania and the implications of such a test in handling malaria cases under field conditions.     

The local-clock permutation test: a simple test to compare rates of molecular evolution on phylogenetic trees

Rates of molecular evolution vary substantially between lineages, and a growing effort is directed at uncovering the causes and consequences of this variation. Comparing local-clocks (rates of molecular evolution estimated from different sets of branches of a phylogenetic tree) is a common tool in this research effort. Here, I show that a commonly used test (the Likelihood Ratio Test, LRT) will not be statistically valid for comparing local-clocks in most cases. Instead, I propose the local-clock permutation test (LCPT), a simple test that can be used to test the significance of differences between local-clocks. The LCPT could also be used to test for differences between any parameter that can be assigned to individual branches on a phylogenetic tree. Using simulated data, I show that the LCPT has good power to detect differences between local-clocks.     

Microsatellite allele sizes: a simple test to assess their significance on genetic differentiation

The mutation process at microsatellite loci typically occurs at high rates and with stepwise changes in allele sizes, features that may introduce bias when using classical measures of population differentiation based on allele identity (e.g., F(ST), Nei's Ds genetic distance). Allele size-based measures of differentiation, assuming a stepwise mutation process [e.g., Slatkin's R(ST), Goldstein et al.'s (deltamu)(2)], may better reflect differentiation at microsatellite loci, but they suffer high sampling variance. The relative efficiency of allele size- vs. allele identity-based statistics depends on the relative contributions of mutations vs. drift to population differentiation. We present a simple test based on a randomization procedure of allele sizes to determine whether stepwise-like mutations contributed to genetic differentiation. This test can be applied to any microsatellite data set designed to assess population differentiation and can be interpreted as testing whether F(ST) = R(ST). Computer simulations show that the test efficiently identifies which of F(ST) or R(ST) estimates has the lowest mean square error. A significant test, implying that R(ST) performs better than F(ST), is obtained when the mutation rate, mu, for a stepwise mutation process is (a) >/= m in an island model (m being the migration rate among populations) or (b) >/= 1/t in the case of isolated populations (t being the number of generations since population divergence). The test also informs on the efficiency of other statistics used in phylogenetical reconstruction [e.g., Ds and (deltamu)(2)], a nonsignificant test meaning that allele identity-based statistics perform better than allele size-based ones. This test can also provide insights into the evolutionary history of populations, revealing, for example, phylogeographic patterns, as illustrated by applying it on three published data sets.     

Relating tree growth to rainfall in Bolivian rain forests: a test for six species using tree ring analysis

Many tropical regions show one distinct dry season. Often, this seasonality induces cambial dormancy of trees, particularly if these belong to deciduous species. This will often lead to the formation of annual rings. The aim of this study was to determine whether tree species in the Bolivian Amazon region form annual rings and to study the influence of the total amount and seasonal distribution of rainfall on diameter growth. Ring widths were measured on stem discs of a total of 154 trees belonging to six rain forest species. By correlating ring width and monthly rainfall data we proved the annual character of the tree rings for four of our study species. For two other species the annual character was proved by counting rings on trees of known age and by radiocarbon dating. The results of the climate–growth analysis show a positive relationship between tree growth and rainfall in certain periods of the year, indicating that rainfall plays a major role in tree growth. Three species showed a strong relationship with rainfall at the beginning of the rainy season, while one species is most sensitive to the rainfall at the end of the previous growing season. These results clearly demonstrate that tree ring analysis can be successfully applied in the tropics and that it is a promising method for various research disciplines.     

Biogeography of species richness gradients: linking adaptive traits,demography and diversification

Here we review how adaptive traits contribute to the emergence and maintenance of species richness gradients through their influence on demographic and diversification processes. We start by reviewing how demographic dynamics change along species richness gradients. Empirical studies show that geographical clines in population parameters and measures of demographic variability are frequent along latitudinal and altitudinal gradients. Demographic variability often increases at the extremes of regional species richness gradients and contributes to shape these gradients. Available studies suggest that adaptive traits significantly influence demographic dynamics, and set the limits of species distributions. Traits related to thermal tolerance, resource use, phenology and dispersal seem to play a significant role. For many traits affecting demography and/or diversification processes, complex mechanistic approaches linking genotype, phenotype and fitness are becoming progressively available. In several taxa, species can be distributed along adaptive trait continuums, i.e. a main axis accounting for the bulk of inter‐specific variation in some correlated adaptive traits. It is shown that adaptive trait continuums can provide useful mechanistic frameworks to explain demographic dynamics and diversification in species richness gradients. Finally, we review the existence of sequences of adaptive traits in phylogenies, the interactions of adaptive traits and community context, the clinal variation of traits across geographical gradients, and the role of adaptive traits in determining the history of dispersal and diversification of clades. Overall, we show that the study of demographic and evolutionary mechanisms that shape species richness gradients clearly requires the explicit consideration of adaptive traits. To conclude, future research lines and trends in the field are briefly outlined.     

Factors influencing diversification in angiosperms: at the crossroads of intrinsic and extrinsic traits

Recent studies indicate that both key innovations and available area influence species richness in angiosperms. Available area has been observed to have the greatest effect, however, and appears to alter the "carrying capacity" of a lineage rather than alter diversification rates. Here, we review and weigh the evidence of predictors of angiosperm diversification and further dissect how area can place ecological limits on diversification of angiosperms, specifically addressing the following: (1) theoretical mechanisms by which particular intrinsic and extrinsic traits may affect diversification in angiosperm families; (2) evidence that the amount of available area determines the ecological limits on lineages; and (3) geographical distribution of diversification hotspots in angiosperms, concentrating on the effects of zygomorphy, noncontiguous area, and latitude. While we found that dispersal to numerous noncontiguous areas is most important in spurring diversification, diversification of tropical and zygomorphic families appears to be elevated by the generation of more species per given area.     

Evolutionary diversification of bruchine beetles: climate-dependent traits and development associated with pest status

A number of insect species infest human households and stored foods and products, leading to their designation as pests. Until recently, little was known about the factors driving the evolution of pests that feed on stored dry foods. Here, I review the effects of changes in climate and species interactions on the evolution and ecology of beetles that feed on dried seeds/grains. My review focuses on evidence that the host utilization by part of the species in the subfamily Bruchinae (Chrysomelidae) is a preadaptation for utilizing stored dry seeds and grains, thus leading to their status as a pest. These and other stored product pest beetles retain a higher percentage of water in their body, relative to the water content of their diet, than beetles that feed on fresh crops. I review the studies that have documented adaptation, acclimation and polyphenetic response to high temperatures and desiccation and/or made direct comparisons between these traits between developmental stages, populations and among higher taxonomic groups. Finally, I review evidence for the effects of environmental change on insect host-parasitoid and competitor assemblages.     

Monogenic traits are not simple: lessons from phenylketonuria.

The classification of genetic disease into chromosomal, monogenic and multifactorial categories is an oversimplification. Phenylketonuria (PKU) is a classic 'monogenic' autosomal recessive disease in which mutation at the human PAH locus was deemed sufficient to explain the impaired function of the enzyme phenylalanine hydroxylase (enzymic phenotype), the attendant hyperphenylalaninemia (metabolic phenotype) and the resultant mental retardation (cognitive phenotype). In the era of molecular genetics, expectations for a consistently close correlation between the mutant genotype and variant phenotype have been somewhat disappointed, and PKU is used here to illustrate how and why this might be the case. So-called monogenic traits do, indeed, conform to long-accepted ideas about the expression of 'major' loci and their importance in determining parameters of phenotype, but the associated features are as complex, in their own ways, as those in so-called complex traits.     

Genetics of personalities: no simple answers for complex traits

Identifying the genes that underlie phenotypic variation in natural populations, and assessing the consequences of polymorphisms at these loci for individual fitness are major objectives in evolutionary biology. Yet, with the exception of a few success stories, little progress has been made, and our understanding of the link between genotype and phenotype is still in its infancy. For example, although body length in humans is largely genetically determined, with heritability estimates greater than 0.8, massive genome‐wide association studies (GWAS) have only been able to account for a very small proportion of this variation ( Gudbjartsson et al. 2008 ). If it is so difficult to explain the genetics behind relatively ‘simple’ traits, can we envision that it will at all be possible to find genes underlying complex behavioural traits in wild non‐model organisms? Some notable examples suggest that this can indeed be a worthwhile endeavour. Recently, the circadian rhythm gene Clock has been associated with timing of breeding in a wild blue tit population ( Johnsen et al. 2007 ; Liedvogel et al. 2009 ) and the Pgi gene to variation in dispersal and flight endurance in Glanville fritillary butterflies ( Niitepold et al. 2009 ). A promising candidate gene for influencing complex animal personality traits, also known as behavioural syndromes ( Sih et al. 2004 ), is the dopamine receptor D4 (DRD4) gene. Within the last decade, polymorphisms in this gene have been associated with variation in novelty seeking and exploration behaviour in a range of species, from humans to great tits ( Schinka et al. 2002 ; Fidler et al. 2007 ). In this issue, Korsten et al. (2010) attempt to replicate this previously observed association in wild‐living birds, and test for the generality of the association between DRD4 and personality across a number of European great tit populations.     

Using functional traits to predict grassland ecosystem change: a mathematical test of the response-and-effect trait approach

The role of plant community structure and plant functional traits for above- and belowground carbon (C) fluxes was studied for 2 years in a mesocosm experiment with grassland monoliths, using continuous gas exchange measurements and soil analyses. Here we test the response-and-effect trait hypothesis, by applying a mathematical framework used to predict changes in C fluxes after a change in disturbance through the community response ( R ) and effect ( E ) traits. Monoliths were extracted from two contrasted long-term field treatments (high vs. low grazing disturbance) and exposed to both low and high (simulated grazing) disturbance during a 2 years experiment. Carbon dioxide exchanges were measured continuously in an open flow system. Net ecosystem productivity and ecosystem C balance were positively correlated at low disturbance with plant species richness. Aboveground net primary productivity (ANPP) and soil C sequestration were, however, unrelated to these variables. Community aggregated leaf (specific leaf area, leaf dry-matter content) and root and rhizome (specific length, tissue density, diameter) traits responded ( R ) significantly to changes in disturbance, indicating an increased dominance of conservative plant growth strategies at low compared with high disturbance. Applying the mathematical framework, ANPP was predicted by distribution of leaf traits within the community (functional divergence), while mean root and rhizome traits had significant effects ( E ) on soil C sequestration, irrespective of the experimental disturbance and of the year. According to highly significant linear regression models, between 6% and 61% of the transient changes in soil C sequestration resulted from community root and rhizome (response-and-effect) traits after a change in disturbance.     

Relating molecular flexibility to function: a case study of tubulin

Microtubules (MT), along with a variety of associated motor proteins, are involved in a range of cellular functions including vesicle movement, chromosome segregation, and cell motility. MTs are assemblies of heterodimeric proteins, alpha beta-tubulins, the structure of which has been determined by electron crystallography of zinc-induced, pacilitaxel-stabilized tubulin sheets. These data provide a basis for examining relationships between structural features and protein function. Here, we study the fluctuation dynamics of the tubulin dimer with the aim of elucidating its functional motions relevant to substrate binding, polymerization/depolymerization and MT assembly. A coarse-grained model, harmonically constrained according to the crystal structure, is used to explore the global dynamics of the dimer. Our results identify six regions of collective motion, comprised of structurally close but discontinuous sequence fragments, observed only in the dimeric form, dimerization being a prerequisite for domain identification. Boundaries between regions of collective motions appear to act as linkages, found primarily within secondary-structure elements that lack sequence conservation, but are located at minima in the fluctuation curve, at positions of hydrophobic residues. Residue fluctuations within these domains identify the most mobile regions as loops involved in recognition of the adjacent regions. The least mobile regions are associated with nucleotide binding sites where lethal mutations occur. The functional coupling of motions between and within regions identifies three global motions: torsional and wobbling movements, en bloc, between the alpha- and beta-tubulin monomers, and stretching longitudinally. Further analysis finds the antitumor drug pacilitaxel (TaxotereR) to reduce flexibility in the M loop of the beta-tubulin monomer; an effect that may contribute to tightening lateral interactions between protofilaments assembled into MTs. Our analysis provides insights into relationships between intramolecular tubulin movements of MT organization and function.