Optimal outgroup analysis

We present and critically examine a statistical criterion for the selection of outgroup taxa for rooting evolutionary trees. The criterion is the amount of phylogenetic signal for the ingroup when the states of the candidate outgroup taxa are assumed to be plesiomorphic relative to the ingroup for the purpose of measuring plesiomorphy content of the outgroup taxon. A statistical measure of rooted, ingroup signal was subjected to a suite of critical tests which indicate that it provides a proxy measure of plesiomorphy content. As the evolutionary distance between the ingroup ancestral node and outgroup taxa increases, the tree-independent measure of signal decreases, tracking the decay in plesiomorphy content and the increase in convergence to the ingroup states. We show that a priori generalizations about optimal outgroup taxon sampling strategies are likely to be misleading, and that testing for the suitability of available outgroup taxon sampling in specific instances is warranted. Software for optimal outgroup analysis is available.     

Phylogenetic inference under the pure drift model

When pairwise genetic distances are used for phylogenetic reconstruction, it is usually assumed that the genetic distance between two taxa contains information about the time after the two taxa diverged. As a result, upon an appropriate transformation if necessary, the distance usually can be fitted to a linear model such that it is expressed as the sum of lengths of all branches that connect the two taxa in a given phylogeny. This kind of distance is referred to as "additive distance." For a phylogenetic tree exclusively driven by random genetic drift, genetic distances related to coancestry coefficients (theta XY) between any two taxa are more suitable. However, these distances are fundamentally different from the additive distance in that coancestry does not contain any information about the time after two taxa split from a common ancestral population; instead, it reflects the time before the two taxa diverged. In other words, the magnitude of theta XY provides information about how long the two taxa share the same evolutionary pathways. The fundamental difference between the two kinds of distances has led to a different algorithm of evaluating phylogenetic trees when theta XY and related distance measures are used. Here we present the new algorithm using the ordinary- least-squares approach but fitting to a different linear model. This treatment allows genetic variation within a taxon to be included in the model. Monte Carlo simulation for a rooted phylogeny of four taxa has verified the efficacy and consistency of the new method. Application of the method to human population was demonstrated.      

The coexistence of hybrid and parental Daphnia: the role of parasites

Parasite driven time-lagged negative frequency-dependent selection of hosts has been studied in natural populations by following changes in host genotype frequencies over time. However, such dynamics have not been considered at higher taxonomic levels, for example, between parental species and their hybrids. In a field study on a Daphnia hybrid system, we observed that one Daphnia taxon first was relatively under-infected, but became over-infected after a strong increase in frequency. This finding is consistent with the idea of parasite evolution towards the most frequent host taxon. In two experiments, we investigated whether the assumptions made by a model of negative frequency-dependent selection apply to our host taxa system. First, we showed that the parasite can change the outcome of taxa competition and secondly, we confirmed that the over-infection of one host taxon observed in the field has a genetic basis. Our results indicate that the incorporation of host-parasite interactions at the species level may allow us to gain a more complete picture of forces driving dynamic taxa coexistence in Daphnia hybrid systems. More generally, we suggest that if hybrids coexist in sympatry with parental taxa, the infection patterns as observed under natural conditions may be rather temporal and unstable.     

Maximizing phylogenetic diversity in biodiversity conservation: Greedy solutions to the Noah's Ark problem

The Noah's Ark Problem (NAP) is a comprehensive cost-effectiveness methodology for biodiversity conservation that was introduced by Weitzman (1998) and utilizes the phylogenetic tree containing the taxa of interest to assess biodiversity. Given a set of taxa, each of which has a particular survival probability that can be increased at some cost, the NAP seeks to allocate limited funds to conserving these taxa so that the future expected biodiversity is maximized. Finding optimal solutions using this framework is a computationally difficult problem to which a simple and efficient "greedy" algorithm has been proposed in the literature and applied to conservation problems. We show that, although algorithms of this type cannot produce optimal solutions for the general NAP, there are two restricted scenarios of the NAP for which a greedy algorithm is guaranteed to produce optimal solutions. The first scenario requires the taxa to have equal conservation cost; the second scenario requires an ultrametric tree. The NAP assumes a linear relationship between the funding allocated to conservation of a taxon and the increased survival probability of that taxon. This relationship is briefly investigated and one variation is suggested that can also be solved using a greedy algorithm.     

Optimal taxonomic groups for biodiversity assessment: a meta‐analytic approach

A fundamental decision in biodiversity assessment is the selection of one or more study taxa, a choice that is often made using qualitative criteria such as historical precedent, ease of detection, or available technical or taxonomic expertise. A more robust approach would involve selecting taxa based on the a priori expectation that they will provide the best possible information on unmeasured groups, but data to inform such hypotheses are often lacking. Using a global meta‐analysis, we quantified the proportion of variability that each of 12 taxonomic groups (at the Order level or above) explained in the richness or composition of other taxa. We then applied optimization to matrices of pairwise congruency to identify the best set of complementary surrogate groups. We found that no single taxon was an optimal surrogate for both the richness and composition of unmeasured taxa if we used simple methods to aggregate congruence data between studies. In contrast, statistical methods that accounted for well‐known drivers of cross‐taxon congruence (spatial extent, grain size, and latitude) lead to the prioritization of similar surrogates for both species richness and composition. Advanced statistical methods were also more effective at describing known ecological relationships between taxa than simple methods, and show that congruence is typically highest between taxonomically and functionally dissimilar taxa. Birds and vascular plants were most frequently selected by our algorithm as surrogates for other taxonomic groups, but the extent to which any one taxon was the ‘optimal’ choice of surrogate for other biodiversity was highly context‐dependent. In the absence of other information – such as in data‐poor areas of the globe, and under limited budgets for monitoring or assessment – ecologists can use our results to assess which taxa are most likely to reflect the distribution of the richness or composition of ‘total’ biodiversity.     

EST-SSRs as a resource for population genetic analyses

Simple-sequence repeats (SSRs) have increasingly become the marker of choice for population genetic analyses. Unfortunately, the development of traditional 'anonymous' SSRs from genomic DNA is costly and time-consuming. These problems are further compounded by a paucity of resources in taxa that lack clear economic importance. However, the advent of the genomics age has resulted in the production of vast amounts of publicly available DNA sequence data, including large collections of expressed sequence tags (ESTs) from a variety of different taxa. Recent research has revealed that ESTs are a potentially rich source of SSRs that reveal polymorphisms not only within the source taxon, but in related taxa, as well. In this paper, we review what is known about the transferability of EST-SSRs from one taxon to another with particular reference to the potential of these markers to facilitate population genetic studies. As an example of the utility of these resources, we then cross-reference existing EST databases against lists of rare, endangered and invasive plant species and conclude that half of all suitable EST databases could be exploited for the population genetic analysis of species of conservation concern. We then discuss the advantages and disadvantages of EST-SSRs in the context of population genetic applications.     

Relationships among the major lineages of Dictyoptera: the effect of outgroup selection on dictyopteran tree topology

Abstract Dictyoptera, comprising Blattaria, Isoptera, and Mantodea, are diverse in appearance and life history, and are strongly supported as monophyletic. We downloaded COII, 16S, 18S, and 28S sequences of 39 dictyopteran species from GenBank. Ribosomal RNA sequences were aligned manually with reference to secondary structure. We included morphological data (maximum of 175 characters) for 12 of these taxa and for an additional 15 dictyopteran taxa (for which we had only morphological data). We had two datasets, a 59‐taxon dataset with five outgroup taxa, from Phasmatodea (2 taxa), Mantophasmatodea (1 taxon), Embioptera (1 taxon), and Grylloblattodea (1 taxon), and a 62‐taxon dataset with three additional outgroup taxa from Plecoptera (1 taxon), Dermaptera (1 taxon) and Orthoptera (1 taxon). We analysed the combined molecular?morphological dataset using the doublet and MK models in Mr Bayes , and using a parsimony heuristic search in paup . Within the monophyletic Mantodea, Mantoida is recovered as sister to the rest of Mantodea, followed by Chaeteessa; the monophyly of most of the more derived families as defined currently is not supported. We recovered novel phylogenetic hypotheses about the taxa within Blattodea (following Hennig, containing Isoptera). Unique to our study, one Bayesian analysis places Polyphagoidea as sister to all other Dictyoptera; other analyses and/or the addition of certain orthopteran sequences, however, place Polyphagoidea more deeply within Dictyoptera. Isoptera falls within the cockroaches, sister to the genus Cryptocercus. Separate parsimony analyses of independent gene fragments suggest that gene selection is an important factor in tree reconstruction. When we varied the ingroup taxa and/or outgroup taxa, the internal dictyopteran relationships differed in the position of several taxa of interest, including Cryptocercus, Polyphaga, Periplaneta and Supella. This provides further evidence that the choice of both outgroup and ingroup taxa greatly affects tree topology.     

Physiological performance and mating system in Clarkia (Onagraceae): Does phenotypic selection predict divergence between sister species?

? Premise of the study: The evolution of self-fertilization often occurs in association with other floral, life history, and fitness-related traits. A previous study found that field populations of Clarkia exilis (a predominantly autogamous selfer) and its sister species, Clarkia unguiculata (a facultative outcrosser) differ in mean photosynthetic rates and instantaneous water use efficiency (WUE(i)). Here, we investigate the strength and direction of selection on these traits in multiple populations of each taxon to determine whether natural selection may contribute to the phenotypic differences between them. ? Methods: In spring 2008, we measured instantaneous gas exchange rates in nine populations during vegetative growth (Early) and/or during flowering (Late). We conducted selection gradient analyses and estimated selection differentials within populations and across pooled conspecific populations to evaluate the strength, direction, and consistency of selection on each trait early and late in the season. ? Key results: The direction and relative strength of selection on photosynthetic rates in these taxa corresponds to the phenotypic difference between them; C. exilis has higher photosynthetic rates than C. unguiculata, as well as stronger, more consistent selection favoring rapid photosynthesis throughout the growing season. Patterns of selection on transpiration, WUE(i), and the timing of flowering progression are less consistent with phenotypic differences (or lack thereof) between taxa. ? Conclusions: We detected several examples where selection was consistent with the phenotypic divergence between sister taxa, but there were also numerous instances that were equivocal or in which selection did not predict the realized phenotypic difference between taxa.     

Increased taxon sampling greatly reduces phylogenetic error

Several authors have argued recently that extensive taxon sampling has a positive and important effect on the accuracy of phylogenetic estimates. However, other authors have argued that there is little benefit of extensive taxon sampling, and so phylogenetic problems can or should be reduced to a few exemplar taxa as a means of reducing the computational complexity of the phylogenetic analysis. In this paper we examined five aspects of study design that may have led to these different perspectives. First, we considered the measurement of phylogenetic error across a wide range of taxon sample sizes, and conclude that the expected error based on randomly selecting trees (which varies by taxon sample size) must be considered in evaluating error in studies of the effects of taxon sampling. Second, we addressed the scope of the phylogenetic problems defined by different samples of taxa, and argue that phylogenetic scope needs to be considered in evaluating the importance of taxon-sampling strategies. Third, we examined the claim that fast and simple tree searches are as effective as more thorough searches at finding near-optimal trees that minimize error. We show that a more complete search of tree space reduces phylogenetic error, especially as the taxon sample size increases. Fourth, we examined the effects of simple versus complex simulation models on taxonomic sampling studies. Although benefits of taxon sampling are apparent for all models, data generated under more complex models of evolution produce higher overall levels of error and show greater positive effects of increased taxon sampling. Fifth, we asked if different phylogenetic optimality criteria show different effects of taxon sampling. Although we found strong differences in effectiveness of different optimality criteria as a function of taxon sample size, increased taxon sampling improved the results from all the common optimality criteria. Nonetheless, the method that showed the lowest overall performance (minimum evolution) also showed the least improvement from increased taxon sampling. Taking each of these results into account re-enforces the conclusion that increased sampling of taxa is one of the most important ways to increase overall phylogenetic accuracy.     

Phylogenomics with incomplete taxon coverage: the limits to inference

Background  

Phylogenomic studies based on multi-locus sequence data sets are usually characterized by partial taxon coverage, in which sequences for some loci are missing for some taxa. The impact of missing data has been widely studied in phylogenetics, but it has proven difficult to distinguish effects due to error in tree reconstruction from effects due to missing data per se. We approach this problem using a explicitly phylogenomic criterion of success, decisiveness, which refers to whether the pattern of taxon coverage allows for uniquely defining a single tree for all taxa.     

Polychaete phylogeny based on morphological data – a comparison of current attempts

Annelid phylogeny is one of the largest unresolved problems within the Metazoa. This is due to the enormous age of this taxon and also strongly influenced by the current discussion on the position of the Arthropoda, which traditionally is hypothesized to be the annelid sister taxon. Within the framework of recent discussions on the position of the Annelida, the ground pattern of this taxon is either a clitellate-like, parapodia-less dwelling organism or an organisms that resembles errant polychaetes in having parapodia and gills and probably being a predator. To solve this problem different attempts have been made in the past, cladistic analysis, scenario based plausibility considerations and a successive search for sister taxa base on isolated characters. These attempts are presented and critically discussed. There is at least strong support for the Annelida as wells as for several of its taxa above the level of traditional families; the monophyly of the Polychaeta, however, remains questionable. The term taxon is used here in the sense of group of things that share certain characteristics. Biological taxa are not necessarily monophyletic, although many of them turned out to be. In terms of phylogenetic systematics taxa should be monophyletic.     

A new algorithm for the determination of differential taxa

Question: How can we determine differential taxa in a vegetation data set? Methods: The new algorithm presented here uses an intuitive fidelity threshold based on relative constancy differences. It is tested on a simulated and a real data set. The results of the proposed algorithm are discussed in comparison with other methods used for the determination of differential taxa. Results: The new algorithm defines each taxon in each group of relevés as: (1) positively differentiating, (2) positively‐negatively differentiating, (3) negatively differentiating, or (4) non‐differentiating. Each taxon in a data set may be: (1) positively, positively‐negatively or negatively differentiating for each group in the data set, (2) differentiating for some groups and non‐differentiating for the remaining groups, or (3) non‐differentiating for all groups in the data set. Conclusions: The new algorithm finds the relevé groups that are positively differentiated against other groups that are negatively differentiated. It reveals differentiating structures in the data set and thus makes quantification of the relations among and between different syntaxonomic ranks conceivable. As it distinguishes between different types of differential taxa, it might improve standards of typification in vegetation classification.     

A stepwise algorithm for finding minimum evolution trees

A stepwise algorithm for reconstructing minimum evolution (ME) trees from evolutionary distance data is proposed. In each step, a taxon that potentially has a neighbor (another taxon connected to it with a single interior node) is first chosen and then its true neighbor searched iteratively. For m taxa, at most (m-1)!/2 trees are examined and the tree with the minimum sum of branch lengths (S) is chosen as the final tree. This algorithm provides simple strategies for restricting the tree space searched and allows us to implement efficient ways of dynamically computing the ordinary least squares estimates of S for the topologies examined. Using computer simulation, we found that the efficiency of the ME method in recovering the correct tree is similar to that of the neighbor-joining method (Saitou and Nei 1987). A more exhaustive search is unlikely to improve the efficiency of the ME method in finding the correct tree because the correct tree is almost always included in the tree space searched with this stepwise algorithm. The new algorithm finds trees for which S values may not be significantly different from that of the ME tree if the correct tree contains very small interior branches or if the pairwise distance estimates have large sampling errors. These topologies form a set of plausible alternatives to the ME tree and can be compared with each other using statistical tests based on the minimum evolution principle. The new algorithm makes it possible to use the ME method for large data sets.      

Spatial and seasonal variability in the trophic role of aquatic insects: An assessment of functional feeding group applicability

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Absence of population-level phenotype matching in an obligate pollination mutualism

Coevolution is thought to promote evolutionary change between demes that ultimately results in speciation. If this is the case, then we should expect to see similar patterns of trait matching and phenotypic divergence between populations and between species in model systems for coevolution. As measures of divergence are frequently only available at one scale (population level or taxon level), this contention is rarely tested directly. Here, we use the case of co-divergence between different varieties of Joshua tree Yucca brevifolia (Agavaceae) and their obligate pollinators, two yucca moths (Tegeticula spp. Prodoxidae), to test for trait matching between taxa and among populations. Using model selection, we show that there is trait matching between mutualists at the taxon level, but once we account for differences between taxa, there is no indication of trait matching in local populations. This result differs from similar studies in other coevolving systems. We hypothesize that this discrepancy arises because coevolution in obligate mutualisms favours divergence less strongly than coevolution in other systems, such as host–parasite interactions.     

Budgeted Phylogenetic Diversity on Circular Split Systems

In the last 15 years, Phylogenetic Diversity (PD) has gained interest in the community of conservation biologists as a surrogate measure for assessing biodiversity. We have recently proposed two approaches to select taxa for maximizing PD, namely PD with budget constraints and PD on split systems. In this paper, we will unify these two strategies and present a dynamic programming algorithm to solve the unified framework of selecting taxa with maximal PD under budget constraints on circular split systems. An improved algorithm will also be given if the underlying split system is a tree.     

Maximum parsimony on subsets of taxa

In this paper we investigate mathematical questions concerning the reliability (reconstruction accuracy) of Fitch's maximum parsimony algorithm for reconstructing the ancestral state given a phylogenetic tree and a character. In particular, we consider the question whether the maximum parsimony method applied to a subset of taxa can reconstruct the ancestral state of the root more accurately than when applied to all taxa, and we give an example showing that this indeed is possible. A surprising feature of our example is that ignoring a taxon closer to the root improves the reliability of the method. On the other hand, in the case of the two-state symmetric substitution model, we answer affirmatively a conjecture of Li, Steel and Zhang which states that under a molecular clock the probability that the state at a single taxon is a correct guess of the ancestral state is a lower bound on the reconstruction accuracy of Fitch's method applied to all taxa.     

Measuring inferential importance of taxa using taxon influence indices

Assessing the importance of different taxa for inferring evolutionary history is a critical, but underutilized, aspect of systematics. Quantifying the importance of all taxa within a dataset provides an empirical measurement that can establish a ranking of extant taxa for ecological study and/or quantify the relative importance of newly announced or redescribed specimens to enable the disentangling of novelty and inferential influence. Here, we illustrate the use of taxon influence indices through analysis of both molecular and morphological datasets, introducing a modified Bayesian approach to the taxon influence index that accounts for model and topological uncertainty. Quantification of taxon influence using the Bayesian approach produced clear rankings for both dataset types. Bayesian taxon rankings differed from maximum likelihood (ML)‐derived rankings from a mitogenomic dataset, and the highest ranking taxa exhibited the largest interquartile range in influence estimate, suggesting variance in the estimate must be taken into account when the ranking of taxa is the feature of interest. Application of the Bayesian taxon influence index to a recent morphological analysis of the Tully Monster (Tullimonstrum) reveals that it exhibits consistently low inferential importance across two recent treatments of the taxon with alternative character codings. These results lend support to the idea that taxon influence indices may be robust to character coding and therefore effective for morphological analyses. These results underscore a need for the development of approaches to, and application of, taxon influence analyses both for the purpose of establishing robust rankings for future inquiry and for explicitly quantifying the importance of individual taxa. Quantifying the importance of individual taxa refocuses debates in morphological studies from questions of character choice/significance and taxon sampling to explicitly analytical techniques, and guides discussion of the context of new discoveries.