Taxon influence index: assessing taxon-induced incongruities in phylogenetic inference

Death is on Our Side: Paleontological Data Drastically Modify Phylogenetic Hypotheses

Fossils are the only remaining evidence of the majority of species that have ever existed, providing a direct window into events in evolutionary history that shaped the diversification of life on Earth. Phylogenies underpin our ability to make sense of evolution but are routinely inferred using only data available from living organisms. Although extinct taxa have been shown to add crucial information for inferring macroevolutionary patterns and processes (such as ancestral states, paleobiogeography and diversification dynamics), the role fossils play in reconstructing phylogeny is controversial. Since the early years of phylogenetic systematics, different studies have dismissed the impact of fossils due to their incompleteness, championed their ability to overturn phylogenetic hypotheses or concluded that their behavior is indistinguishable from that of extant taxa. Based on taxon addition experiments on empirical data matrices, we show that the inclusion of paleontological data has a remarkable effect in phylogenetic inference. Incorporating fossils often (yet not always) induces stronger topological changes than increasing sampling of extant taxa. Fossils also produce unique topological rearrangements, allowing the exploration of regions of treespace that are never visited by analyses of only extant taxa. Previous studies have proposed a suite of explanations for the topological behavior of fossils, such as their retention of unique morphologies or their ability to break long branches. We develop predictive models that demonstrate that the possession of distinctive character state combinations is the primary predictor of the degree of induced topological change, and that the relative impact of taxa (fossil and extant) can be predicted to some extent before any phylogenetic analysis. Our results bolster the consensus of recent empirical studies by showing the unique role of paleontological data in phylogenetic inference, and provide the first quantitative assessment of its determinants, with broad consequences for the design of taxon sampling in both morphological and total-evidence analyses. [phylogeny, morphology, fossils, parsimony, Bayesian inference.]

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.

Split-specific bootstrap measures for quantifying phylogenetic stability and the influence of taxon selection

Assessing the robustness of an inferred phylogeny is an important element of phylogenetics. This is typically done with measures of stabilities at the internal branches and the variation of the positions of the leaf nodes. The bootstrap support for branches in maximum parsimony, distance and maximum likelihood estimation, or posterior probabilities in Bayesian inference, measure the uncertainty about a branch due to the sampling of the sites from genes or sampling genes from genomes. However, these measures do not reveal how taxon sampling affects branch support and the effects of taxon sampling on the estimated phylogeny. An internal branch in a phylogenetic tree can be viewed as a split that separates the taxa into two nonempty complementary subsets. We develop several split-specific measures of stability determined from bootstrap support for quartets. These include BPtaxon_split (average bootstrap percentage [BP] for all quartets involving a taxon within a split), BPsplit (BPtaxon_split averaged over taxa), BPtaxon (BPtaxon_split averaged over splits) and RBIC-taxon (average BP over all splits after removing a taxon). We also develop a pruned-tree distance metric. Application of our measures to empirical and simulated data illustrate that existing measures of overall stability can fail to detect taxa that are the primary source of a split-specific instability. Moreover, we show that the use of many reduced sets of quartets is important in being able to detect the influence of joint sets of taxa rather than individual taxa. These new measures are valuable diagnostic tools to guide taxon sampling in phylogenetic experimental design.

Resolving the phylogeny of a speciose spider group, the family Linyphiidae (Araneae)

For high-level molecular phylogenies, a comprehensive sampling design is a key factor for not only improving inferential accuracy, but also for maximizing the explanatory power of the resulting phylogeny. Two standing problems in molecular phylogenies are the unstable placements of some deep and long branches, and the phylogenetic relationships shown by robust supported clades conflict with recognized knowledge. Empirical and theoretical studies suggest that increasing taxon sampling is expected to ameliorate, if not resolve, both problems; however, sometimes neither the current taxonomic system nor the established phylogeny can provide sufficient information to guide additional sampling design. We examined the phylogeny of the spider family Linyphiidae, and selected ingroup species based on epigynal morphology, which can be reconstructed in a phylogenetic context. Our analyses resulted in seven robustly supported clades within linyphiids. The placements of four deep and long branches are sensitive to variations in both outgroup and ingroup sampling, suggesting the possibility of long branch attraction artifacts. Results of ancestral state reconstruction indicate that successive state transformations of the epigynal plate are associated with early cladogenetic events in linyphiid diversification. Representatives of different subfamilies were mixed together within well supported clades and examination revealed that their defining characters, as per traditional taxonomy, are homoplastic. Furthermore, our results demonstrated that increasing taxon sampling produced a more informative framework, which in turn helps to study character evolution and interpret the relationships among linyphiid lineages. Additional defining characters are needed to revise the linyphiid taxonomic system based on our phylogenetic hypothesis.

One misdated sequence of rabbit hemorrhagic disease virus prevents accurate estimation of its nucleotide substitution rate

BACKGROUND

The literature is ripe with phylogenetic estimates of nucleotide substitution rates, especially of measurably evolving species such as RNA viruses. However, it is not known how robust these rate estimates are to inaccuracies in the data, particularly in sampling dates that are used for molecular clock calibration. Here we report on the rate of evolution of the emerging pathogen Rabbit hemorrhagic disease virus (RHDV), which has significantly different rates of evolution for the same outer capsid (VP60) gene published in the literature. In an attempt to reconcile the conflicting data and further elucidate details of RHDV 's evolutionary history, we undertook fresh Bayesian analyses and employed jackknife control methods to produce robust substitution rate and time to most recent common ancestor (TMRCA) estimates for RHDV based on the VP60 and RNA-dependent RNA polymerase genes.

RESULTS

Through these control methods, we were able to identify a single misdated taxon, a passaged lab strain used for vaccine production, which was responsible for depressing the RHDV capsid gene's rate of evolution by 65%. Without this isolate, the polymerase and the capsid protein genes had nearly identical rates of evolution: 1.90x10-3 nucleotide substitutions/site/year, ns/s/y, (95% highest probability density (HPD) 1.25x10-3-2.55x10-3) and 1.91x10-3 ns/s/y (95% HPD 1.50x10-3-2.34x10-3), respectively.

CONCLUSIONS

After excluding the misdated taxon, both genes support a significantly higher substitution rate as well as a relatively recent emergence of RHDV, and obviate the need for previously hypothesized decades of unobserved diversification of the virus. The control methods show that using even one misdated taxon in a large dataset can significantly skew estimates of evolutionary parameters and suggest that it is better practice to use smaller datasets composed of taxa with unequivocal isolation dates. These jackknife controls would be useful for future tip-calibrated rate analyses that include taxa with ambiguous dates of isolation.