Phylogenetic relationships and divergence times of Charadriiformes genera: multigene evidence for the Cretaceous origin of at least 14 clades of shorebirds

Comparative study of character evolution in the shorebirds is presently limited because the phylogenetic placement of some enigmatic genera remains unclear. We therefore used Bayesian methods to obtain a well-supported phylogeny of 90 recognized genera using 5 kb of mitochondrial and nuclear sequences. The tree comprised three major clades: Lari (gulls, auks and allies plus buttonquails) as sister to Scolopaci (sandpipers, jacanas and allies), and in turn sister to Charadrii (plovers, oystercatchers and allies), as in previous molecular studies. Plovers and noddies were not recovered as monophyletic assemblages, and the Egyptian plover Pluvianus is apparently not a plover. Molecular dating using multiple fossil constraints suggests that the three suborders originated in the late Cretaceous between 79 and 102 Mya, and at least 14 lineages of modern shorebirds survived the mass extinction at the K/T boundary. Previous difficulties in determining the phylogenetic relationships of enigmatic taxa reflect the fact that they are well-differentiated relicts of old, genus-poor lineages. We refrain from suggesting systematic revisions for shorebirds at this time because gene trees may fail to recover the species tree when long branches are connected to deep, shorter branches, as is the case for some of the enigmatic taxa.     

Information-theoretic indices and an approximate significance test for testing the molecular clock hypothesis with genetic distances

Distance-based phylogenetic methods are widely used in biomedical research. However, distance-based dating of speciation events and the test of the molecular clock hypothesis are relatively underdeveloped. Here I develop an approximate test of the molecular clock hypothesis for distance-based trees, as well as information-theoretic indices that have been used frequently in model selection, for use with distance matrices. The results are in good agreement with the conventional sequence-based likelihood ratio test. Among the information-theoretic indices, AICu is the most consistent with the sequence-based likelihood ratio test. The confidence in model selection by the indices can be evaluated by bootstrapping. I illustrate the usage of the indices and the approximate significance test with both empirical and simulated sequences. The tests show that distance matrices from protein gel electrophoresis and from genome rearrangement events do not violate the molecular clock hypothesis, and that the evolution of the third codon position conforms to the molecular clock hypothesis better than the second codon position in vertebrate mitochondrial genes. I outlined evolutionary distances that are appropriate for phylogenetic reconstruction and dating.     

Simulating and detecting autocorrelation of molecular evolutionary rates among lineages

Evolutionary timescales can be estimated from genetic data using phylogenetic methods based on the molecular clock. To account for molecular rate variation among lineages, a number of relaxed‐clock models have been developed. Some of these models assume that rates vary among lineages in an autocorrelated manner, so that closely related species share similar rates. In contrast, uncorrelated relaxed clocks allow all of the branch‐specific rates to be drawn from a single distribution, without assuming any correlation between rates along neighbouring branches. There is uncertainty about which of these two classes of relaxed‐clock models are more appropriate for biological data. We present an R package, NELSI, that allows the evolution of DNA sequences to be simulated according to a range of clock models. Using data generated by this package, we assessed the ability of two Bayesian phylogenetic methods to distinguish among different relaxed‐clock models and to quantify rate variation among lineages. The results of our analyses show that rate autocorrelation is typically difficult to detect, even when there is complete taxon sampling. This provides a potential explanation for past failures to detect rate autocorrelation in a range of data sets.     

Flies on thistles: support for synchronous speciation?

Synchronous speciation of hosts and herbivorous insects predicts a congruent topology of host and insect phylogenies and similar evolutionary ages of host and insect taxa. To test these predictions for the specialized herbivorous fly genus Urophora (Diptera: Tephritidae), we used three different approaches. (i) We generated a phylogenetic tree of 11 European Urophora species from allozyme data and constructed a phylogeny of their hosts from published sources. Superimposing the Urophora tree on the host-plant tree we found no evidence for general congruence. (ii) We correlated genetic distances (Nei distances) of the host plants vs. the genetic distances of associated Urophora species. Overall, the relationship was not positive. Nevertheless, for some pairs of Urophora species and host plants genetic distances were in the same order of magnitude. (iii) We collected allozyme data for pairs of thistle taxa and pairs of herbivores on thistles together with independent time estimates. With these data we calibrated a molecular clock. There was a non-linear relationship between phylogenetic age and genetic distance, rendering the dating of deep events in thistle–insect evolution difficult. Nevertheless the derived molecular clock showed that the split of insect taxa lagged behind the split of hosts.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 775–783.     

Rates of molecular evolution in bacteria are relatively constant despite spore dormancy

Rates of molecular evolution are known to vary considerably among lineages, partially due to differences in life-history traits such as generation time. The generation-time effect has been well documented in some eukaryotes, but its prevalence in prokaryotes is unknown. "Because many species of Firmicute bacteria spend long periods of time as metabolically dormant spores, which could result in fewer DNA substitutions per unit time, they present an excellent system for testing predictions of the molecular clock hypothesis." To test whether spore-forming bacteria evolve more slowly than their non-spore-forming relatives, I used phylogenetic methods to determine if there were differences in rates of amino acid substitution between spore-forming and non-spore-forming lineages of Firmicute bacteria. Although rates of evolution do vary among lineages, I find no evidence for an effect of spore-formation on evolutionary rate and, furthermore, evolutionary rates are similar to those calculated for enteric bacteria. These results support the notion that variation in generation time does not affect evolutionary rates in bacterial lineages.     

Why do species vary in their rate of molecular evolution?

Despite hopes that the processes of molecular evolution would be simple, clock-like and essentially universal, variation in the rate of molecular evolution is manifest at all levels of biological organization. Furthermore, it has become clear that rate variation has a systematic component: rate of molecular evolution can vary consistently with species body size, population dynamics, lifestyle and location. This suggests that the rate of molecular evolution should be considered part of life-history variation between species, which must be taken into account when interpreting DNA sequence differences between lineages. Uncovering the causes and correlates of rate variation may allow the development of new biologically motivated models of molecular evolution that may improve bioinformatic and phylogenetic analyses.     

Power of the concentrated changes test for correlated evolution

The concentrated changes test (CCT) calculates the probability that changes in a binary character are distributed randomly on the branches of a cladogram. This test is used to examine hypotheses of correlated evolution, especially cases where changes in the state of one character influence changes in the state of another character. The test may be sensitive to the addition of branches that lack either trait of interest (white branches). To examine the effects of the proportion of white branches and of tree topology on the CCT probability, we conducted a simulation analysis using a series of randomly generated 100-taxon trees, in addition to a nearly perfectly balanced (symmetrical) and a completely imbalanced (asymmetrical) 100-taxon tree. Using two models of evolution (gains only, or gains and losses), we evolved character pairs randomly onto these trees to simulate cases where (1) characters evolve independently (i.e., no correlation among the traits) or (2) all changes in the dependent character occur on branches containing the independent trait (i.e., a strong correlation among the traits). This allowed us to evaluate the sensitivity of the CCT to type I and type II errors, respectively. In the simulations, the CCT did not appear to be overly sensitive to the inclusion of white branches (low likelihood of type I error with both CCT probabilities < 0.05 and < 0.01). However, the CCT was susceptible to type II error when the proportion of white branches was < 20%. The test was also sensitive to tree shape and was positively correlated to Colless's tree imbalance statistic I. Finally, the CCT responded differently for simulations where only gains were allowed and those where both gains and losses were permitted. These results indicate that the CCT is unlikely to detect a correlation between characters when no such correlation exists. However, when a trait can be gained but not lost, the CCT is conservative and may fail to detect true correlations among traits (increased type II error). Determination of the sampling universe (the taxa included in the comparative analysis) can strongly influence the probability of making such type II errors. We suggest guidelines to circumvent these limitations.     

Positive selection operates continuously on hemagglutinin during evolution of H3N2 human influenza A virus

It has been proposed that antigenic evolution of hemagglutinin 1 (HA1) for H3N2 human influenza A virus was punctuated. In the population genetic analysis, however, it was controversial whether positive selection operated on HA1 in a punctuated manner for the branches of the phylogenetic tree where transitions to new antigenic clusters occurred (C branches), or continuously. In the molecular evolutionary analysis, positive selection was detected for the trunk (T) branches but the relationship between antigenic evolution and positive selection was unclear. Here molecular evolutionary analysis was conducted to examine natural selection operating on HA1 of H3N2 human influenza A virus by dividing HA1 into epitopes A-E and other sites, as well as dividing the phylogenetic tree into the C branches overlapping with the T branches (C-T branches), those not overlapping with the T branches (C-NT branches), the T branches not overlapping with the C branches (NC-T branches), and other branches (NC-NT branches). Positive selection was detected for C, T, and NC-T branches, whereas evolution for the NC-NT branches appeared to be mainly neutral. Positive selection appeared to have operated throughout the trunk, which covered the entire time period of the phylogenetic tree, suggesting that positive selection operated continuously on HA1 during evolution of H3N2 human influenza A virus.     

A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock

Current understanding of the diversification of birds is hindered by their incomplete fossil record and uncertainty in phylogenetic relationships and phylogenetic rates of molecular evolution. Here we performed the first comprehensive analysis of mitogenomic data of 48 vertebrates, including 35 birds, to derive a Bayesian timescale for avian evolution and to estimate rates of DNA evolution. Our approach used multiple fossil time constraints scattered throughout the phylogenetic tree and accounts for uncertainties in time constraints, branch lengths, and heterogeneity of rates of DNA evolution. We estimated that the major vertebrate lineages originated in the Permian; the 95% credible intervals of our estimated ages of the origin of archosaurs (258 MYA), the amniote-amphibian split (356 MYA), and the archosaur-lizard divergence (278 MYA) bracket estimates from the fossil record. The origin of modern orders of birds was estimated to have occurred throughout the Cretaceous beginning about 139 MYA, arguing against a cataclysmic extinction of lineages at the Cretaceous/Tertiary boundary. We identified fossils that are useful as time constraints within vertebrates. Our timescale reveals that rates of molecular evolution vary across genes and among taxa through time, thereby refuting the widely used mitogenomic or cytochrome b molecular clock in birds. Moreover, the 5-Myr divergence time assumed between 2 genera of geese (Branta and Anser) to originally calibrate the standard mitochondrial clock rate of 0.01 substitutions per site per lineage per Myr (s/s/l/Myr) in birds was shown to be underestimated by about 9.5 Myr. Phylogenetic rates in birds vary between 0.0009 and 0.012 s/s/l/Myr, indicating that many phylogenetic splits among avian taxa also have been underestimated and need to be revised. We found no support for the hypothesis that the molecular clock in birds "ticks" according to a constant rate of substitution per unit of mass-specific metabolic energy rather than per unit of time, as recently suggested. Our analysis advances knowledge of rates of DNA evolution across birds and other vertebrates and will, therefore, aid comparative biology studies that seek to infer the origin and timing of major adaptive shifts in vertebrates.     

Tree imbalance causes a bias in phylogenetic estimation of evolutionary timescales using heterochronous sequences

Phylogenetic estimation of evolutionary timescales has become routine in biology, forming the basis of a wide range of evolutionary and ecological studies. However, there are various sources of bias that can affect these estimates. We investigated whether tree imbalance, a property that is commonly observed in phylogenetic trees, can lead to reduced accuracy or precision of phylogenetic timescale estimates. We analysed simulated data sets with calibrations at internal nodes and at the tips, taking into consideration different calibration schemes and levels of tree imbalance. We also investigated the effect of tree imbalance on two empirical data sets: mitogenomes from primates and serial samples of the African swine fever virus. In analyses calibrated using dated, heterochronous tips, we found that tree imbalance had a detrimental impact on precision and produced a bias in which the overall timescale was underestimated. A pronounced effect was observed in analyses with shallow calibrations. The greatest decreases in accuracy usually occurred in the age estimates for medium and deep nodes of the tree. In contrast, analyses calibrated at internal nodes did not display a reduction in estimation accuracy or precision due to tree imbalance. Our results suggest that molecular‐clock analyses can be improved by increasing taxon sampling, with the specific aims of including deeper calibrations, breaking up long branches and reducing tree imbalance.     

The likelihood node density effect and consequences for evolutionary studies of molecular rates

Many molecular phylogenies show longer root-to-tip path lengths in species-rich groups, encouraging hypotheses linking cladogenesis with accelerated molecular evolution. However, the pattern can also be caused by an artifact called the node density effect (NDE): this effect occurs when the method used to reconstruct a tree underestimates multiple hits that would have been revealed by extra nodes, leading to longer root-to-tip path lengths in clades with more terminal taxa. Here we use a twofold approach to demonstrate that maximum likelihood and Bayesian methods also suffer from the NDE known to affect parsimony. First, simulations deliberately mismatching the simulation and reconstruction models show that the greater the model disparity, the greater the gap between actual and reconstructed tree lengths, and the greater the NDE. Second, taxon sampling manipulation with empirical data shows that NDE can still be present when using optimized models: across 12 datasets, 70 out of 109 sister path comparisons showed significant evidence of NDE. Unless the model fairly accurately reconstructs the real tree length-and given the complexity of real sequence evolution this may be uncommon -- it will consistently produce a node density artifact. At commonly encountered divergence levels, a 10% underestimation of tree length results in > or = 80% of simulated phylogenies showing a positive NDE. Bayesian trees have a slight but consistently stronger effect. This pervasive methodological artifact increases apparent rate heterogeneity, and can compromise investigations of factors influencing molecular evolutionary rate that use path lengths in topologically asymmetric trees.     

Sociality and the rate of molecular evolution

The molecular clock does not tick at a uniform rate in all taxa but may be influenced by species characteristics. Eusocial species (those with reproductive division of labor) have been predicted to have faster rates of molecular evolution than their nonsocial relatives because of greatly reduced effective population size; if most individuals in a population are nonreproductive and only one or few queens produce all the offspring, then eusocial animals could have much lower effective population sizes than their solitary relatives, which should increase the rate of substitution of "nearly neutral" mutations. An earlier study reported faster rates in eusocial honeybees and vespid wasps but failed to correct for phylogenetic nonindependence or to distinguish between potential causes of rate variation. Because sociality has evolved independently in many different lineages, it is possible to conduct a more wide-ranging study to test the generality of the relationship. We have conducted a comparative analysis of 25 phylogenetically independent pairs of social lineages and their nonsocial relatives, including bees, wasps, ants, termites, shrimps, and mole rats, using a range of available DNA sequences (mitochondrial and nuclear DNA coding for proteins and RNAs, and nontranslated sequences). By including a wide range of social taxa, we were able to test whether there is a general influence of sociality on rates of molecular evolution and to test specific predictions of the hypothesis: (1) that social species have faster rates because they have reduced effective population sizes; (2) that mitochondrial genes would show a greater effect of sociality than nuclear genes; and (3) that rates of molecular evolution should be correlated with the degree of sociality. We find no consistent pattern in rates of molecular evolution between social and nonsocial lineages and no evidence that mitochondrial genes show faster rates in social taxa. However, we show that the most highly eusocial Hymenoptera do have faster rates than their nonsocial relatives. We also find that social parasites (that utilize the workers from related species to produce their own offspring) have faster rates than their social relatives, which is consistent with an effect of lower effective population size on rate of molecular evolution. Our results illustrate the importance of allowing for phylogenetic nonindependence when conducting investigations of determinants of variation in rate of molecular evolution.     

Positive correlations between molecular and morphological rates of evolution

The existence of positive associations between rates of molecular and morphological evolution (calculated from branch lengths of phylogenetic trees reconstructed using molecular and morphological characters, respectively) is important to issues of neutrality in sequence evolution, phylogenetic reconstructions assuming neutrality, and evolutionary genotype-phenotype mapping. Rates correlate positively when including branches leading to extant species (tips). Excluding tips, trends are similar, but statistical significances decrease systematically. This is due to (a) lower statistical power (excluding tips reduces sample sizes), and (b) rates are solely calculated from inaccurately reconstructed character states of extinct ancestral species, and this noise decreases correlation strengths. Correlations between molecular and morphological rates of evolution increase as more morphological characters are included for phylogenetic reconstruction. Sequence lengths apparently affect correlations along similar principles. Analyses of plant phylogenies confirm those from animals: sampling biases decrease correlations between molecular and morphological rates of evolution. Results confirm that genotype and phenotype are linked, and suggest adaptive components for molecular evolution. The discussion stresses the difficulties associated with analyses and conclusions based on data deduced from phylogenetic reconstruction.     

Testing the molecular clock: molecular and paleontological estimates of divergence times in the Echinoidea (Echinodermata)

The phylogenetic relationships of 46 echinoids, with representatives from 13 of the 14 ordinal-level clades and about 70% of extant families commonly recognized, have been established from 3 genes (3,226 alignable bases) and 119 morphological characters. Morphological and molecular estimates are similar enough to be considered suboptimal estimates of one another, and the combined data provide a tree that, when calibrated against the fossil record, provides paleontological estimates of divergence times and completeness of their fossil record. The order of branching on the cladogram largely agrees with the stratigraphic order of first occurrences and implies that their fossil record is more than 85% complete at family level and at a resolution of 5-Myr time intervals. Molecular estimates of divergence times derived from applying both molecular clock and relaxed molecular clock models are concordant with estimates based on the fossil record in up to 70% of cases, with most concordant results obtained using Sanderson's semiparametric penalized likelihood method and a logarithmic-penalty function. There are 3 regions of the tree where molecular and fossil estimates of divergence time consistently disagree. Comparison with results obtained when molecular divergence dates are estimated from the combined (morphology + gene) tree suggests that errors in phylogenetic reconstruction explain only one of these. In another region the error most likely lies with the paleontological estimates because taxa in this region are demonstrated to have a very poor fossil record. In the third case, morphological and paleontological evidence is much stronger, and the topology for this part of the molecular tree differs from that derived from the combined data. Here the cause of the mismatch is unclear but could be methodological, arising from marked inequality of molecular rates. Overall, the level of agreement reached between these different data and methodological approaches leads us to believe that careful application of likelihood and Bayesian methods to molecular data provides realistic divergence time estimates in the majority of cases (almost 80% in this specific example), thus providing a remarkably well-calibrated phylogeny of a character-rich clade of ubiquitous marine benthic invertebrates.     

General properties and phylogenetic utilities of nuclear ribosomal DNA and mitochondrial DNA commonly used in molecular systematics

To choose one or more appropriate molecular markers or gene regions for resolving a particular systematic question among the organisms at a certain categorical level is still a very difficult process. The primary goal of this review, therefore, is to provide a theoretical information in choosing one or more molecular markers or gene regions by illustrating general properties and phylogenetic utilities of nuclear ribosomal DNA (rDNA) and mitochondrial DNA (mtDNA) that have been most commonly used for phylogenetic researches. The highly conserved molecular markers and/or gene regions are useful for investigating phylogenetic relationships at higher categorical levels (deep branches of evolutionary history). On the other hand, the hypervariable molecular markers and/or gene regions are useful for elucidating phylogenetic relationships at lower categorical levels (recently diverged branches). In summary, different selective forces have led to the evolution of various molecular markers or gene regions with varying degrees of sequence conservation. Thus, appropriate molecular markers or gene regions should be chosen with even greater caution to deduce true phylogenetic relationships over a broad taxonomic spectrum.     

Monte Carlo simulation in phylogenies: An application to test the constancy of evolutionary rates

Monte Carlo simulation has commonly been used in phylogenetic studies to test different tree-reconstruction methods, and consequently, its application for testing evolutionary models can be considered as a natural extension of this usage. Repetitive simulation of a given evolutionary process, under the restrictions imposed by the model to be tested, along a determinate tree topology allow the estimate of probability distributions for the desired parameters. Next, the phylogenetic tree can be reconstructed again without the constraints of the model, and the parameter of interest, derived from this tree, can be compared to the corresponding probability distribution derived from the restricted, simulated trees. As an example we have used Monte Carlo simulation to test the constancy of evolutionary rates in a set of cytochrome-c protein sequences. Correspondence to: J. Dopazo     

Differentiation trees,a junk DNA molecular clock,and the evolution of neoteny in salamanders

Obligate neotenic salamanders die if forced to metamorphose. We suggest that this can be explained by assuming: 1) their “excess” DNA is “junk” DNA; 2) the “adult” specifying portion of the DNA becomes junk DNA and is available for repeated duplication. This suggests a “new” junk DNA molecular clock. We obtain remarkable agreement in “predicting” the amount of DNA per nucleus in present day non-obligate neotene salamanders from this molecular clock. These observatons are consistent with the idea that the development of these animals is describable in terms of differentiation trees whose branches (gene cascades) corresponding to adult somatic tissues accumulate deleterious mutations over evolutionary time. We show that the amount of DNA per nucleus increases linearly with the phylogenetic age of salamander families. The lack of constraints by natural selection, on unused adult branches, may account for the large amount of so-called “junk DNA” in obligate neotenic salamanders. The effects of this excess DNA, via increased cell size, suggest a positive feedback, ecophysiological explanation for such junk DNA: adaptation to cool water environments is enhanced by the lower metabolism associated with more DNA, larger cells and slower developmental time.     

Purifying Selection Determines the Short-Term Time Dependency of Evolutionary Rates in SARS-CoV-2 and pH1N1 Influenza

High-throughput sequencing enables rapid genome sequencing during infectious disease outbreaks and provides an opportunity to quantify the evolutionary dynamics of pathogens in near real-time. One difficulty of undertaking evolutionary analyses over short timescales is the dependency of the inferred evolutionary parameters on the timespan of observation. Crucially, there are an increasing number of molecular clock analyses using external evolutionary rate priors to infer evolutionary parameters. However, it is not clear which rate prior is appropriate for a given time window of observation due to the time-dependent nature of evolutionary rate estimates. Here, we characterize the molecular evolutionary dynamics of SARS-CoV-2 and 2009 pandemic H1N1 (pH1N1) influenza during the first 12 months of their respective pandemics. We use Bayesian phylogenetic methods to estimate the dates of emergence, evolutionary rates, and growth rates of SARS-CoV-2 and pH1N1 over time and investigate how varying sampling window and data set sizes affect the accuracy of parameter estimation. We further use a generalized McDonald–Kreitman test to estimate the number of segregating nonneutral sites over time. We find that the inferred evolutionary parameters for both pandemics are time dependent, and that the inferred rates of SARS-CoV-2 and pH1N1 decline by ∼50% and ∼100%, respectively, over the course of 1 year. After at least 4 months since the start of sequence sampling, inferred growth rates and emergence dates remain relatively stable and can be inferred reliably using a logistic growth coalescent model. We show that the time dependency of the mean substitution rate is due to elevated substitution rates at terminal branches which are 2–4 times higher than those of internal branches for both viruses. The elevated rate at terminal branches is strongly correlated with an increasing number of segregating nonneutral sites, demonstrating the role of purifying selection in generating the time dependency of evolutionary parameters during pandemics.     

An empirical test of the midpoint rooting method

The outgroup method is widely used to root phylogenetic trees. An accurate root indication, however, strongly depends on the availability of a proper outgroup. An alternate rooting method is the midpoint rooting (MPR). In this case, the root is set at the midpoint between the two most divergent operational taxonomic units. Although the midpoint rooting algorithm has been extensively used, the efficiency of this method in retrieving the correct root remains untested. In the present study, we empirically tested the success rate of the MPR in obtaining the outgroup root for a given phylogenetic tree. This was carried out by eliminating outgroups in 50 selected data sets from 33 papers and rooting the trees with the midpoint method. We were thus able to compare the root position retrieved by each method. Data sets were separated into three categories with different root consistencies: data sets with a single outgroup taxon (54% success rate for MPR), data sets with multiple outgroup taxa that showed inconsistency in root position (82% success rate), and data sets with multiple outgroup taxa in which root position was consistent (94% success rate). Interestingly, the more consistent the outgroup root is, the more successful MPR appears to be. This is a strong indication that the MPR method is valuable, particularly for cases where a proper outgroup is unavailable.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 669–674.     

A guide through a family of phylogenetic dissimilarity measures among sites

Ecological studies have now gone beyond measures of species turnover towards measures of phylogenetic and functional dissimilarity. This change of perspective has a main objective: disentangling the processes that drive species distributions from local to broad scales. A fundamental difference between phylogenetic and functional analyses is that phylogeny is intrinsically dependent on a tree‐like structure whereas functional data can, most of time, only be forced to adhere a tree structure, not without some loss of information. When the branches of a phylogenetic tree have lengths, then each evolutionary unit on these branches can be considered as a basic entity on which dissimilarities among sites should be measured. Several of the recent measures of phylogenetic dissimilarities among sites thus are traditional dissimilarity indices where species are replaced by evolutionary units. The resulting indices were named PD‐dissimilarity indices, in reference to early work on the phylogenetic diversity (PD) measure. Here I review and compare indices and ordination approaches that, although first developed to analyse the differences in the species compositions of sites, can be adapted to describe PD‐dissimilarities among sites. Using simulations of species distributions along environmental gradients, I compare indices, associated with permutation tests and null models, in their ability to reveal existing phylogenetic patterns along the gradients. As an illustration, I show that the amount of bat PD‐dissimilarities along a disturbance gradient in Selva Lacandona of Chiapas, Mexico is dependent on whether species' abundance is considered, and on the PD‐dissimilarity index used. Overall, the family of PD‐dissimilarity indices has a critical potential for future analyses of phylogenetic diversity as it benefits from decades of research on the measure of species dissimilarity. I provide clues to help to choose among many potential indices, identifying which indices satisfy minimal basic properties, and analysing their sensitivity to abundance, size, diversity and joint absences.