[Show abstract][Hide abstract] ABSTRACT: 1. The prevalence of phylogenetic niche conservatism (PNC) in nature is still a conflicting issue. Disagreement arises from confusion over its precise definition and the variety of approaches to measure its prevalence. Recent work highlighted that common measures of PNC strongly depend on the assumptions of the underlying model of niche evolution. However, this warning has not been well recognized in the applied literature and questionable approaches are still frequently applied.
2. The aim of this paper is to draw attention to the assumptions underlying commonly applied simple measures of PNC. We used a series of simulations to illustrate how misleading results can be if assumptions of niche evolution are violated, that the violation of assumptions is a common phenomenon and that testing assumptions requires in-depth pre-test.
3. We conclude that the seemingly simple measures of PNC, such as phylogenetic signal and evolutionary rate, are not so easy to apply if one accounts for the necessity to test model assumptions. In addition, these measures can be difficult to interpret. The common assumption that strong phylogenetic signal indicates PNC will be often invalid. In addition, the interpretation of some measures, e.g. the conclusion that evolutionary rate is slow enough to indicate PNC, requires a comparison with another clade, another trait or well-developed null model assumptions and thus additional data.
4. We suggest that studies investigating PNC should always compare alternative evolutionary models, and that model comparisons should in particular include flexible niche evolution models such as multiple-optima OU models, although these are computational intensive. These models are directly inherited from the concept of macro-evolutionary adaptive landscape, and can indicate PNC either by relative few peak shifts or by narrow peaks in the adaptive landscape. A test of PNC thus requires comparing these parameters of the macroevolutionary landscape between clades or time periods.
5. The general prevalence of PNC in nature should be evaluated only based on studies keeping up to the high standards of communicating the used definition of PNC, testing the assumptions made in the modelling approaches and including newly developed models in a model comparison approach.
[Show abstract][Hide abstract] ABSTRACT: Protected areas (PAs) are pivotal tools for biodiversity conservation on the Earth. Europe has had an extensive protection system since Natura 2000 areas were created in parallel with traditional parks and reserves. However, the extent to which this system covers not only taxonomic diversity but also other biodiversity facets, such as evolutionary history and functional diversity, has never been evaluated. Using high-resolution distribution data of all European tetrapods together with dated molecular phylogenies and detailed trait information, we first tested whether the existing European protection system effectively covers all species and in particular, those with the highest evolutionary or functional distinctiveness. We then tested the ability of PAs to protect the entire tetrapod phylogenetic and functional trees of life by mapping species' target achievements along the internal branches of these two trees. We found that the current system is adequately representative in terms of the evolutionary history of amphibians while it fails for the rest. However, the most functionally distinct species were better represented than they would be under random conservation efforts. These results imply better protection of the tetrapod functional tree of life, which could help to ensure long-term functioning of the ecosystem, potentially at the expense of conserving evolutionary history.
Philosophical Transactions of The Royal Society B Biological Sciences 02/2015; 370(1662). DOI:10.1098/rstb.2014.0005 · 6.31 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Different assembly processes drive the spatial structure of meta-communities (β- diversity). Recently, functional and phylogenetic diversities have been suggested as indicators of these assembly processes. Assuming that diversity is a good proxy for niche overlap, high β-diversity along environmental gradients should be the result of environmental filtering while low β- diversity should stem from competitive interactions. So far studies trying to disentangle the relative importance of these assembly processes provided mixed results. One reason for this may be that these studies often rely on a single measure of diversity and thus implicitly make a choice on how they account for species relative abundances and how species similarities are captured by functional traits or phylogeny.
Here, we tested the effect of gradually scaling the importance of dominance (the weight given to dominant vs. rare species) and species similarity (the weight given to small vs. large similarities) on resulting β-diversity patterns of an alpine plant meta-community. To this end, we combined recent extensions of the Hill numbers framework with Pagel’s phylogenetic tree transformation approach. We included functional (based on the Leaf-Height-Seed spectrum) and phylogenetic facets of β-diversity in our analysis and explicitly accounted for effects of environmental and spatial covariates.
We found that functional β-diversity was high when the same weight was given to dominant vs. rare species and to large vs. small species’ similarities. In contrast, phylogenetic β-diversity was low when greater weight was given to dominant species and small species' similarities. Those results suggested that different environments along the gradients filtered different species according to their functional traits, while, the same competitive lineages dominated communities across the gradients.
Our results highlight that functional vs. phylogenetic facets, presence-absence vs. abundance structure and different weights of species’ dissimilarity provide complementary and important information on the drivers of meta-community structure. By utilizing the full extent of information provided by the flexible frameworks of Hill numbers and Pagel's tree transformation, we propose a new approach to disentangle the patterns resulting from different assembly processes.
[Show abstract][Hide abstract] ABSTRACT: Despite considerable efforts devoted to investigate the community assembly processes driving plant invasions, few general conclusions have been drawn so far. Three main processes, generally acting as successive filters, are thought to be of prime importance. The invader has to disperse (1st filter) into a suitable environment (2nd filter) and succeed in establishing in recipient communities through competitive interactions (3rd filter) using two strategies: competition avoidance by the use of different resources (resource opportunity), or competitive exclusion of native species. Surprisingly, despite the general consensus on the importance of investigating these three processes and their interplay, they are usually studied independently. Here we aim to analyse these three filters together, by including them all: abiotic environment, dispersal and biotic interactions, into models of invasive species distributions. We first propose a suite of indices (based on species functional dissimilarities) supposed to reflect the two competitive strategies (resource opportunity and competition exclu-sion). Then, we use a set of generalised linear models to explain the distribution of seven herbaceous invaders in natural communities (using a large vegetation database for the French Alps containing 5,000 community-plots). Finally, we measure the relative importance of compet-itive interaction indices, identify the type of coexistence mechanism involved and how this varies along envi-ronmental gradients. Adding competition indices signif-icantly improved model's performance, but neither resource opportunity nor competitive exclusion were common strategies among the seven species. Overall, we show that combining environmental, dispersal and biotic information to model invasions has excellent potential for improving our understanding of invader success.
[Show abstract][Hide abstract] ABSTRACT: 1.The α, β, γ diversity decomposition methodology is commonly used to investigate changes in diversity over space or time but rarely conjointly. However, with the ever-increasing availability of large-scale biodiversity monitoring data, there is a need for a sound methodology capable of simultaneously accounting for spatial and temporal changes in diversity.2.Using the properties of Chao's index, we adapted Rao's framework of diversity decomposition between orthogonal dimensions to a multiplicative α, β, γ decomposition of functional or phylogenetic diversity over space and time, thereby combining their respective properties. We also developed guidelines for interpreting both temporal and spatial β-diversities and their interaction.3.We characterised the range of β-diversity estimates and their relationship to the nested decomposition of diversity. Using simulations, we empirically demonstrated that temporal and spatial β-diversities are independent from each other and from α and γ-diversities when the study design is balanced, but not otherwise. Furthermore, we showed that the interaction term between the temporal and the spatial β-diversities lacked such properties.4.We illustrated our methodology with a case study of the spatio-temporal dynamics of functional diversity in bird assemblages in four regions of France. Based on these data, our method makes it possible to discriminate between regions experiencing different diversity changes in time. Our methodology may therefore be valuable for comparing diversity changes over space and time using large-scale datasets of repeated surveys.This article is protected by copyright. All rights reserved.
Methods in Ecology and Evolution 10/2014; 6(1). DOI:10.1111/2041-210X.12297 · 5.32 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: AimTo reconstruct the historical assembly of the eudicot flora of Mediterranean sierras by examining compositional (CBD), phylogenetic (PBD) and functional (FBD) beta diversity between elevational belts among disjunct mountain ranges (sierras), and relating these measures of turnover to environmental and geographical distances.LocationBaetic ranges, Andalusia, southern Spain.Methods
We compiled eudicot species and subspecies (‘entities’) checklists for three elevational belts within each of eight sierras of Andalusia (‘sites’) and tested for non-random patterns of PBD and FBD of all entities and of endemic entities separately among sites between and within sierras. Multiple regression on distance matrices was used to determine the respective contribution of climate, lithology and geographical distance to CBD, PBD and FBD. Finally, we decomposed PBD into the turnover and nestedness components of beta diversity, and quantified the phylogenetic diversity (PD) within sites.ResultsThe observed PBD and FBD among elevational belts within sierras for all entities were generally higher than expected based on their respective null distributions, whereas CBD among elevational belts within sierras was similar or even lower than between sierras. In contrast, the observed PBD and FBD for endemics were non-significant in most of the comparisons. Temperature-related variables best explained patterns of CBD, PBD and FBD for all entities, whereas lithology and geographical distance were the main drivers of endemic CBD. The observed PBD among elevational belts within sierras was mainly attributable to differences in PD rather than ‘true’ turnover.Main conclusionsThere is strong structuring of plant lineages along elevational gradients in the Baetic range, probably due to habitat filtering acting on life forms and character syndromes that show strong phylogenetic signal. The differentiation of the endemic flora that contributed to the emergence of this western Mediterranean biodiversity hotspot was probably driven by geographical isolation and/or by repeated specialization to contrasting lithologies.
Journal of Biogeography 08/2014; 42(3). DOI:10.1111/jbi.12398 · 4.97 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We investigate patterns of phylogenetic diversity in relation to species diversity for European birds, mammals and amphibians, to evaluate their congruence and highlight areas of particular evolutionary history. We estimate the extent to which the European network of protected areas (PAs) network retains interesting evolutionary history areas for the three groups separately and simultaneously.
Phylogenetic (QEPD) and species diversity (SD) were estimated using the Rao's quadratic entropy at 10' resolution. We determined the regional relationship between QEPD and SD for each taxa with a spatial regression model and used the tails of the residuals (QERES) distribution to identify areas of higher and lower QEPD than predicted. Spatial congruence of biodiversity between groups was assessed with Pearson's correlation. A simple classification scheme allowed building a convergence map where a convergent pixel equalled to a QERES value of the same sign for the 3 groups. This convergence map was overlaid to the current PAs network to estimate the level of protection in convergent pixels and compared it to a null expectation built on 1000 randomization of PAs over the landscape.
QERES patterns across vertebrates show a strong spatial mismatch highlighting different evolutionary histories. Convergent areas represent only 2.7% of the Western Palearctic, with only 8.4% of these areas being covered by the current PAs network while a random distribution would retain 10.4% of them. QERES are unequally represented within PAs: areas with higher QEPD than predicted are better covered than expected, while low QEPD areas are undersampled.
Patterns of diversity strongly diverge between groups of vertebrates in Europe. Although Europe has the world's most extensive PAs network, evolutionary history of terrestrial vertebrates is unequally protected. The challenge is now to reconcile effective conservation planning with a contemporary view of biodiversity integrating multiple facets.
Diversity and Distributions 06/2014; 20(6):674-685. DOI:10.1111/ddi.12186 · 5.47 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Aim Phylogenetic diversity patterns are increasingly being used to better understand the role of ecological and evolutionary processes in community assembly. Here, we quantify how these patterns are influenced by scale choices in terms of spatial and environmental extent and organismic scales. LocationEuropean Alps.
Methods We applied 42 sampling strategies differing in their combination of focal scales. For each resulting sub-dataset, we estimated the phylogenetic diversity of the species pools, phylogenetic α-diversities of local communities, and statistics commonly used together with null models in order to infer non-random diversity patterns (i.e. phylogenetic clustering versus over-dispersion). Finally, we studied the effects of scale choices on these measures using regression analyses.
Results Scale choices were decisive for revealing signals in diversity patterns. Notably, changes in focal scales sometimes reversed a pattern of over-dispersion into clustering. Organismic scale had a stronger effect than spatial and environmental extent. However, we did not find general rules for the direction of change from over-dispersion to clustering with changing scales. Importantly, these scale issues had only a weak influence when focusing on regional diversity patterns that change along abiotic gradients.
Main conclusions Our results call for caution when combining phylogenetic data with distributional data to study how and why communities differ from random expectations of phylogenetic relatedness. These analyses seem to be robust when the focus is on relating community diversity patterns to variation in habitat conditions, such as abiotic gradients. However, if the focus is on identifying relevant assembly rules for local communities, the uncertainty arising from a certain scale choice can be immense. In the latter case, it becomes necessary to test whether emerging patterns are robust to alternative scale choices.
Global Ecology and Biogeography 06/2014; DOI:10.1111/geb.12137 · 7.24 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Patterns of adaptation in response to environmental variation are central to our understanding of biodiversity, but predictions of how and when broad-scale environmental conditions such as climate affect organismal form and function remain incomplete. Succulent plants have evolved in response to arid conditions repeatedly, with various plant organs such as leaves, stems, and roots physically modified to increase water storage. Here we investigate the role played by climate conditions in shaping the evolution of succulent forms in a plant clade endemic to Madagascar and the surrounding islands, part of the hyper-diverse genus Euphorbia (Euphorbiaceae). We used multivariate ordination of 19 climate variables to identify links between particular climate variables and three major forms of succulence - succulent leaves, cactiform stem succulence, and tubers. We then tested the relationship between climatic conditions and succulence, using comparative methods that account for shared evolutionary history. We confirm that plant water storage is associated with the two components of aridity, temperature and precipitation. Cactiform stem succulence, however, is not prevalent in the driest environments, countering the widely held view of cactiforms as desert icons. Instead, leaf succulence and tubers are significantly associated with the lowest levels of precipitation. Our findings provide a clear link between broad-scale climatic conditions and adaptation in land plants, and new insights into the climatic conditions favoring different forms of succulence. This evidence for adaptation to climate raises concern over the evolutionary future of succulent plants as they, along with other organisms, face anthropogenic climate change.
[Show abstract][Hide abstract] ABSTRACT: Evolutionary adaptation is a key driver of species’ range dynamics. Understanding the factors that affect rates of adaptation at range margins is thus crucial for interpreting and predicting changes in species’ ranges. The spatial structure of environmental conditions is one of the determinants of whether and how quickly adaptations occur. However, while landscape structures at range edges are typically complex, most theoretical work has so far focused on relatively simple environmental geometries.Using an individual-based allelic model, we explore the effects of different landscape structures on the rate of adaptation to novel environments and investigate how these structures interact with the genetic architecture of the trait governing adaptation and the dispersal capacity of the considered species. Generally, we find that rapid adaptation is favored by a good match between the coarseness of the trait's genetic architecture (many loci of small effects versus few loci of large effects) and the coarseness of the landscape (abruptness of transitions in environmental conditions). For example, in rugged landscapes, adaptation is quicker for genetic architectures with few loci of large effects, while for shallow gradients the opposite is true. Moreover, dispersal capacities affect the rate of adaptation by modulating the ‘apparent coarseness’ of the landscape: a gradient perceived as smooth by species with limited dispersal capacities appears rather steep for highly dispersive ones. We also find that the distribution of evolving phenotypes strongly depends on the interplay of landscape structure and dispersal capacities, ranging from two distinct phenotypes for most rugged landscapes, over the co-occurrence of an additional third phenotype for highly dispersive species, to the whole range of phenotypes on smooth gradients.By identifying basic factors that drive the fixation probability of newly arising beneficial mutations, we hope to further broaden the understanding of evolutionary adaptation at range margins and, hence, species’ range dynamics.
[Show abstract][Hide abstract] ABSTRACT: Abstract Recent debate on whether climatic niches are conserved through time has focused on how phylogenetic niche conservatism can be measured by deviations from a Brownian motion model of evolutionary change. However, there has been no evaluation of this methodological approach. In particular, the fact that climatic niches are usually obtained from distribution data and are thus heavily influenced by biogeographic factors has largely been overlooked. Our main objective here was to test whether patterns of climatic niche evolution that are frequently observed might arise from neutral dynamics rather than from adaptive scenarios. We developed a model inspired by neutral biodiversity theory, where individuals disperse, compete, and undergo speciation independently of climate. We then sampled the climatic niches of species according to their geographic position and showed that even when species evolve independently of climate, their niches can nonetheless exhibit evolutionary patterns strongly differing from Brownian motion. Indeed, climatic niche evolution is better captured by a model of punctuated evolution with constraints due to landscape boundaries, two features that are traditionally interpreted as evidence for selective processes acting on the niche. We therefore suggest that deviation from Brownian motion alone should not be used as evidence for phylogenetic niche conservatism but that information on phenotypic traits directly linked to physiology is required to demonstrate that climatic niches have been conserved through time.
The American Naturalist 05/2014; 183(5):573-84. DOI:10.1086/675506 · 4.45 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The origins of ecological diversity in continental species assemblages have long intrigued biogeographers. We apply phylogenetic comparative analyses to disentangle the evolutionary patterns of ecological niches in an assemblage of European birds. We compare phylogenetic patterns in trophic, habitat and climatic niche components.
From polygon range maps and handbook data we inferred the realized climatic, habitat and trophic niches of 405 species of breeding birds in Europe. We fitted Pagel's lambda and kappa statistics, and conducted analyses of disparity through time to compare temporal patterns of ecological diversification on all niche axes together. All observed patterns were compared with expectations based on neutral (Brownian) models of niche divergence.
In this assemblage, patterns of phylogenetic signal (lambda) suggest that related species resemble each other less in regard to their climatic and habitat niches than they do in their trophic niche. Kappa estimates show that ecological divergence does not gradually increase with divergence time, and that this punctualism is stronger in climatic niches than in habitat and trophic niches. Observed niche disparity markedly exceeds levels expected from a Brownian model of ecological diversification, thus providing no evidence for past phylogenetic niche conservatism in these multivariate niches. Levels of multivariate disparity are greatest for the climatic niche, followed by disparity of the habitat and the trophic niches.
Phylogenetic patterns in the three niche components differ within this avian assemblage. Variation in evolutionary rates (degree of gradualism, constancy through the tree) and/or non-random macroecological sampling probably lead here to differences in the phylogenetic structure of niche components. Testing hypotheses on the origin of these patterns requires more complete phylogenetic trees of the birds, and extended ecological data on different niche components for all bird species.
Global Ecology and Biogeography 04/2014; 23(4):414-424. DOI:10.1111/geb.12127 · 7.24 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Biological invasions can transform our understanding of how the interplay of historical isolation and contemporary (human-aided) dispersal affects the structure of intraspecific diversity in functional traits, and in turn, how changes in functional traits affect other scales of biological organization such as communities and ecosystems. Because biological invasions frequently involve the admixture of previously isolated lineages as a result of human-aided dispersal, studies of invasive populations can reveal how admixture results in novel genotypes and shifts in functional trait variation within populations. Further, because invasive species can be ecosystem engineers within invaded ecosystems, admixture-induced shifts in the functional traits of invaders can affect the composition of native biodiversity and alter the flow of resources through the system. Thus, invasions represent promising yet under-investigated examples of how the effects of short-term evolutionary changes can cascade across biological scales of diversity. Here, we propose a conceptual framework that admixture between divergent source populations during biological invasions can reorganize the genetic variation underlying key functional traits, leading to shifts in the mean and variance of functional traits within invasive populations. Changes in the mean or variance of key traits can initiate new ecological feedback mechanisms that result in a critical transition from a native ecosystem to a novel invasive ecosystem. We illustrate the application of this framework with reference to a well-studied plant model system in invasion biology and show how a combination of quantitative genetic experiments, functional trait studies, whole ecosystem field studies and modeling can be used to explore the dynamics predicted to trigger these critical transitions.
Ecology and Evolution 04/2014; 4(7):899-910. DOI:10.1002/ece3.966 · 2.32 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Cushion plants have long fascinated botanists for their ability to cope with extreme environments in most mountains and arctic regions of the world. One century ago, a first worldwide catalogue of species forming cushions was published by Hauri and Schröter (Bot Jahrb Syst Pflanzengesch Pflanzengeogr 50:618–656, 1914). Here, we defined a simplified typology of cushion plants and updated the worldwide catalogue of cushion species, along with information on their geographic distribution. This compilation was based on available information in floras and catalogues but also in efloras and virtual encyclopedias, which were screened using automated database queries. We established a list of 1,309 cushion-forming species distributed in 272 genera and 63 families of angiosperms. Compact cushions are represented by 678 species, among which 587 species exhibit a hemispherical shape, and 91 species exhibit a flat to mat shape. We found 398 species forming non-compact hemispherical cushions. The list of cushion species has significantly increased since Hauri and Shröter, due to the description of new species, updated regional inventories, and improved access to electronic databases. Uncertainties in the delineation of the cushion life form are discussed, notably for non-compact growth forms. A website has been launched to display the catalogue and enable a collaborative improvement of the database (http://www.cushionplants.eu/). The distribution of the species is presented on the basis of the world geographical scheme for recording plant distributions and global biodiversity information facility data. This catalogue will serve as a reference database for further analyses on the biogeography and evolutionary history of cushion plants and arctico-alpine biotas.
[Show abstract][Hide abstract] ABSTRACT: Climate and land cover changes are important drivers of the plant species distributions and diversity patterns in mountainous regions. Although the need for a multifaceted view of diversity based on taxonomic, functional and phylogenetic dimensions is now commonly recognized, there are no complete risk assessments concerning their expected changes. In this paper, we used a range of species distribution models in an ensemble-forecasting framework together with regional climate and land cover projections by 2080 to analyze the potential threat for more than 2500 plant species at high resolution (2.5 × 2.5 km) in the French Alps. We also decomposed taxonomic, functional and phylogenetic diversity facets into α and β components and analyzed their expected changes by 2080. Overall, plant species threats from climate and land cover changes in the French Alps were expected to vary depending on the species’ preferred altitudinal vegetation zone, rarity, and conservation status. Indeed, rare species and species of conservation concern were the ones projected to experience less severe change, and also the ones being the most efficiently preserved by the current network of protected areas. Conversely, the three facets of plant diversity were also projected to experience drastic spatial re-shuffling by 2080. In general, the mean α-diversity of the three facets was projected to increase to the detriment of regional β-diversity, although the latter was projected to remain high at the montane-alpine transition zones. Our results show that, due to a high-altitude distribution, the current protection network is efficient for rare species, and species predicted to migrate upward. Although our modeling framework may not capture all possible mechanisms of species range shifts, our work illustrates that a comprehensive risk assessment on an entire floristic region combined with functional and phylogenetic information can help delimitate future scenarios of biodiversity and better design its protection.
[Show abstract][Hide abstract] ABSTRACT: Despite the recognized joint impact of climate and land cover change on facets of biodiversity and their associated functions, risk assessments have primarily evaluated impacts on species ranges and richness. Here we quantify the sensitivity of the functional structure of European avian assemblages to changes in both regional climate and land cover. We combine species range forecasts with functional-trait information. We show that species sensitivity to environmental change is randomly distributed across the functional tree of the European avifauna and that functionally unique species are not disproportionately threatened by 2080. However, projected species range changes will modify the mean species richness and functional diversity of bird diets and feeding behaviours. This will unequally affect the spatial structure of functional diversity, leading to homogenization across Europe. Therefore, global changes may alter the functional structure of species assemblages in the future in ways that need to be accounted for in conservation planning.
[Show abstract][Hide abstract] ABSTRACT: Since the ever-increasing availability of phylogenetic informative data, the last decade has seen an upsurge of ecological studies incorporating information on evolutionary relationships among species. However, detailed species-level phylogenies are still lacking for many large groups and regions, which are necessary for comprehensive large-scale eco-phylogenetic analyses. Here, we provide a dataset of 100 dated phylogenetic trees for all European tetrapods based on a mixture of supermatrix and supertree approaches. Phylogenetic inference was performed separately for each of the main Tetrapoda groups of Europe except mammals (i.e. amphibians, birds, squamates and turtles) by means of maximum likelihood (ML) analyses of supermatrix applying a tree constraint at the family (amphibians and squamates) or order (birds and turtles) levels based on consensus knowledge. For each group, we inferred 100 ML trees to be able to provide a phylogenetic dataset that accounts for phylogenetic uncertainty, and assessed node support with bootstrap analyses. Each tree was dated using penalized-likelihood and fossil calibration. The trees obtained were well-supported by existing knowledge and previous phylogenetic studies. For mammals, we modified the most complete supertree dataset available on the literature to include a recent update of the Carnivora clade. As a final step, we merged the phylogenetic trees of all groups to obtain a set of 100 phylogenetic trees for all European Tetrapoda species for which data was available (91%). We provide this phylogenetic dataset (100 chronograms) for the purpose of comparative analyses, macro-ecological or community ecology studies aiming to incorporate phylogenetic information while accounting for phylogenetic uncertainty.