Phylogenetic Dependence Research Articles

Thermal tolerance and the importance of microhabitats for Andean frogs in the context of land use and climate change.

Global warming is having impacts across the Tree of Life. Understanding species' physiological sensitivity to temperature change and how they relate to local temperature variation in their habitats is crucial to determining vulnerability to global warming. We ask how species' vulnerability varies across habitats and elevations, and how climatically buffered microhabitats can contribute to reduce their vulnerability. We measured thermal sensitivity (critical thermal maximum-CTmax ) of 14 species of Pristimantis frogs inhabiting young and old secondary, and primary forests in the Colombian Andes. Exposure to temperature stress was measured by recording temperature in the understorey and across five microhabitats. We determined frogs' current vulnerability across habitats, elevations and microhabitats accounting for phylogeny and then ask how vulnerability varies under four warming scenarios: +1.5, +2, +3 and +5°C. We found that CTmax was constant across species regardless of habitat and elevation. However, species in young secondary forests are expected to become more vulnerable because of increased exposure to higher temperatures. Microhabitat variation could enable species to persist within their thermal temperature range as long as regional temperatures do not surpass +2°C. The effectiveness of microhabitat buffering decreases with a 2-3°C increase, and is almost null under a 5°C temperature increase. Microhabitats will provide thermal protection to Andean frog communities from climate change by enabling tracking of suitable climates through short distance movement. Conservation strategies, such as managing landscapes by preserving primary forests and allowing regrowth and reconnection of secondary forest would offer thermally buffered microhabitats and aid in the survival of this group.

Constraints on vertebrate range size predict extinction risk

AbstractAimThe only factor in the fossil record that consistently buffers against extinction risk is large geographical range. We ask whether extant vertebrate species with the smallest geographical range for their body size have a higher extinction risk, and thus whether the lower bound of the modern range–body size relationship could serve as an effective conservation prioritization tool.LocationGlobal in scope.Time periodModern.Major taxa studiedSix classes of vertebrates.MethodsWe compiled a database of geographical range, body size and extinction risk for six vertebrate classes (n = 26,076). We characterized the shape of the relationship between geographical range and body size for each class, using 90% and 10% quantile regression to describe the upper and lower bounds, respectively. We then evaluated the degree of extinction vulnerability of species at the lower bound of the regression using generalized linear mixed models. All analyses accounted for phylogenetic dependence between related species.ResultsThe relationships between species ranges and body sizes were generally positive at both the upper and the lower bounds, and segmented (nonlinear) relationships were common. Despite this variability, species near the lower boundary of the relationship were more often in higher extinction risk categories, and this remained true when the role of range size in the International Union for Conservation of Nature Red Listing criteria was accounted for.Main conclusionsVariability in the upper and lower bounds of the range–body size relationship suggests that some classes of vertebrates exhibit combinations of ranges and body sizes that might not reflect historical patterns. Nonetheless, the range–body size relationship remains a reliable and useful predictor of extinction risk, more so than range size does alone. The range–body size relationship could therefore be used to track the trajectories of species towards or away from an extinction threshold and allow the tracking of how different human activities alter the range–body size relationship.

Recent Trends in Research on the Genetic Diversity of Plants: Implications for Conservation

Genetic diversity and its distribution, both within and between populations, may be determined by micro-evolutionary processes, such as the demographic history of populations, natural selection, and gene flow. In plants, indices of genetic diversity (e.g., k, h and π) and structure (e.g., FST) are typically inferred from sequences of chloroplast markers. Given the recent advances and popularization of molecular techniques for research in population genetics, phylogenetics, phylogeography, and ecology, we adopted a scientometric approach to compile evidence on the recent trends in the use of cpDNA sequences as markers for the analysis of genetic diversity in botanical studies, over the years. We also used phylogenetic modeling to assess the relative contribution of relatedness or ecological and reproductive characters to the genetic diversity of plants. We postulated that genetic diversity could be defined not only by microevolutionary factors and life history traits, but also by relatedness, so that species more closely related phylogenetically would have similar genetic diversities. We found a clear tendency for an increase in the number of studies over time, confirming the hypothesis that the advances in the area of molecular genetics have supported the accumulation of data on the genetic diversity of plants. However, we found that the vast majority of these data have been produced by Chinese authors, and refer specifically to populations of Chinese plants. Most of the data on genetic diversity have been obtained for species in the International Union for Conservation of Nature (IUCN) category NE (Not Evaluated), which indicates a relative lack of attention on threatened species. In general, we observed very high FST values in the groups analyzed and, as we focused primarily on species that have not been evaluated by the IUCN, the number of plant species that are threatened with extinction may be much greater than that indicated by the listing of this organization. We also found that the number of haplotypes (k) was influenced by the type of geographic distribution of the plant, while haplotype diversity (h) was affected by the type of flower, and the fixation index (FST), by the type of habitat. The plant species most closely-related phylogenetically have similar levels of genetic diversity. Overall, then, it will important to consider phylogenetic dependence in future studies that evaluate the effects of life-history traits on plant genetic diversity.

The influence of warming on the biogeographic and phylogenetic dependence of herbivore-plant interactions.

Evolutionary experience and the phylogenetic relationships of plants have both been proposed to influence herbivore–plant interactions and plant invasion success. However, the direction and magnitude of these effects, and how such patterns are altered with increasing temperature, are rarely studied. Through laboratory functional response experiments, we tested whether the per capita feeding efficiency of an invasive generalist herbivore, the golden apple snail, Pomacea canaliculata, is dependent on the biogeographic origin and phylogenetic relatedness of host plants, and how increasing temperature alters these dependencies. The feeding efficiency of the herbivore was highest on plant species with which it had no shared evolutionary history, that is, novel plants. Further, among evolutionarily familiar plants, snail feeding efficiency was higher on those species more closely related to the novel plants. However, these biogeographic dependencies became less pronounced with increasing temperature, whereas the phylogenetic dependence was unaffected. Collectively, our findings indicate that the susceptibility of plants to this invasive herbivore is mediated by both biogeographic origin and phylogenetic relatedness. We hypothesize that warming erodes the influence of evolutionary exposure, thereby altering herbivore–plant interactions and perhaps the invasion success of plants.

Global patterns of terrestriality in amphibian reproduction

AbstractAimAmphibians exhibit two basic reproductive modes, terrestrial and aquatic, each with different ecophysiological constraints related to evaporative water loss. We hypothesize that these fundamental niche differences will generate strong geographical patterns at the global scale in response to spatial heterogeneity in temperature and water availability.LocationGlobal.Time periodPresent.Major taxa studiedAmphibians.MethodsWe used global distribution maps of 5,434 amphibian species, classified into terrestrial or aquatic breeders, to estimate the occurrence and proportion of terrestrial breeding species per 1° cell. We used multiple regression models to test the relative importance of seven abiotic variables: annual precipitation, annual mean temperature, annual mean relative air humidity, annual mean actual evapotranspiration, availability of lotic and lentic environments and slope. We used residuals autocovariate (RAC) generalized multiple regression models to control for spatial autocorrelation and a spatial vector based on amphibian phylogeny to account for phylogenetic dependencies among cells. Model generality was evaluated by contrasting results between 11 widely recognized world zoogeographical realms.ResultsGlobally, the occurrence of terrestrial breeding species was better explained by temperature followed by total annual rainfall, relative air humidity and terrain slope. In contrast, the proportion of terrestrial breeders was better explained by terrain slope, followed by total rainfall, temperature and relative air humidity. Actual evapotranspiration and the extension of large lotic and lentic water bodies played a minor role. However, the relative importance and even the sign of the regression coefficients varied among realms, revealing different evolutionary pressures.Main conclusionsNiche differences among terrestrial and aquatic breeding amphibian species are reflected in their distinct geographical distribution across the globe. Adequate conditions for terrestrial reproduction to evolve and thrive are reached in distinct ways in different realms. Temperature constraints and slope suggest that reproductive modes will be impacted differently by climate change.

Conspecific and phylogenetic density-dependent survival differs across life stages in two temperate old-growth forests in Northeast China

Factors that control individual survival dynamics are pivotal determinants of forest diversity. Numerous studies have examined the relative importance of habitat variables and neighborhood effects on individual survival, while few studies have examined this importance in different forest types that largely vary topography. We examined the role of conspecific negative density dependence (CNDD), phylogenetic negative density dependence (PNDD) and habitat variables across life stages in two temperate old-growth forests in Northeast China. Using generalized linear mixed models (GLMMs), we tested whether individual survival is related to neighborhood effects and habitat variables. Our results showed that the relative importance of neighborhood effects and habitat variables to focal individual survival varied among life stages and sites. However, the best-fit models for three life stages (with the exception of seedling stage in the BKPF) at both sites all included habitat variables, indicating that these variables contribute to the patterns of focal individual survival. We found evidence of a CNDD effect, and the strength of this effect decreased as the life stages progressed and varied from a negative effect at the seedling stage to a positive one at the adult stage. This result confirms that the importance of CNDD-based survival at the seedling stage plays a particularly significant role in promoting the coexistence of tree species and maintaining forest diversity. We found evidence of PNDD in our forest, and the impact of heterospecific phylogenetic relatedness on focal individual survival was significantly negative; the strength of PNDD increased as the life stages progressed. The CNDD and PNDD widely varied among species, indicating the importance of including the relative abundance, life history strategies and functional traits of species when determining the factors that affect species sensitivity to neighborhood effects. The results of our study demonstrated that CNDD, PNDD and habitat variables all influence the individual survival of these temperate old-growth forests, but the relative importance of these factors vary among life stages and species. Our results highlight the importance of combining multiple species, life stages, functional traits and large-scale studies for investigating elements that affect species coexistence in tree communities.

Seedling density dependence regulated by population density and habitat filtering: Evidence from a mixed primary broad-leaved Korean pine forest in Northeastern China

The effects of distance dependence, negative density dependence (NDD), phylogenetic density dependence, and habitat filtering were integrated to provide additional evidence in temperate forest tree seedling survival. The main focus of this study was to explore how population density and habitat filtering regulate NDD. An approach involving four classes of population density and three classes of soil moisture was tested, including the effect of habitat variables to more accurately evaluate the underlying ecological processes affecting the density dependence of seedlings. NDD is an important mechanism for the maintenance of species diversity across multiple life stages, particularly during seedling recruitment. By regulating specific population structures to maintain species diversity, the effects of density dependence and distance dependence are sometimes difficult to distinguish. Nevertheless, the contribution of NDD to community assembly, relative to other processes such as habitat filtering, remains a subject of debate. Recently, it has been reported that seedling survivals are also negatively correlated with phylogenetic relatedness between neighbors and focal individuals. This effect is known as phylogenetic negative density dependence (PNDD). However, another opposite effect known as phylogenetic positive density dependence (PPDD) has also been reported to exist. The objectives of this study are to examine the following: (i) how population density affects negative density dependence (NDD); (ii) how habitat filtering regulates the NDD; (iii) whether more evidence can be found for PNDD or PPDD and why; and (iv) whether the intensity of negative density dependence is affected by the distance between parent trees and seedlings. The study was conducted in a 20-ha primary mixed broad-leaved Korean pine forest in Changbai Mountain of China. We used generalized linear mixed models to analyze how the seedling survival of 23 woody plant species relates to neighborhoods and habitat variables. Four models were established with and without habitat variables, and two of the four models were used to test how different population densities of focal seedlings and different gradients of habitat variable regulated negative density dependence. The following results were obtained: (1) the strongest conspecific negative density dependence (CNDD) was found within a radius of 15 m; (2) seedling survival were most strongly impacted by the density of conspecific seedling and adult neighbors in habitats with relatively low soil moisture; (3) the effect of seedling-seedling CNDD was especially significant, when densities ranged from 20 to 40 seedlings/4 m2, and (4) there were some evidences of phylogenetic positive density dependence (PPDD), and the effect of seedling-seedling PPDD was increasing with an increase in soil moisture. Our results demonstrate that conspecific negative density dependence played an important role in seedling survival, which is closely related to habitat filtering and population density. However, we found some evidences of phylogenetic positive density dependence. We suggest that future studies of neighborhood density dependence should increase awareness of evolutionary relationships.

Forest tree neighborhoods are structured more by negative conspecific density dependence than by interactions among closely related species

Interactions among neighbors influence the structure of communities of sessile organisms. Closely related species tend to share habitat and resource requirements and to interact with the same mutualists and natural enemies so that the strength of interspecific interactions tends to decrease with evolutionary divergence time. Nevertheless, the degree to which such phylogenetically related ecological interactions structure plant communities remains unclear. Using data from five large mapped forest plots combined with a DNA barcode mega‐phylogeny, we employed an individual‐based approach to assess the collective effects of focal tree size on neighborhood phylogenetic relatedness. Abundance‐weighted average divergence time for all neighbors (ADT_all) and for heterospecific neighbors only (ADT_hetero) were calculated for each individual of canopy tree species. Within local neighborhoods, we found phylogenetic composition changed with focal tree size. Specifically, significant increases in ADT_all with focal tree size were evident at all sites. In contrast, there was no significant change in ADT_hetero with tree size in four of the five sites for both sapling‐sized and all neighbors, even at the smallest neighbourhood scale (0–5 m), suggesting a limited role for phylogeny‐dependent interactions. However, there were inverse relationships between focal tree size and the proportion of heterospecific neighbors belonging to closely related species at some sites, providing evidence for negative phylogenetic density dependence. Overall, our results indicate that negative interaction with conspecifics had a much greater impact on neighborhood assemblages than interactions among closely related species and could contribute to community structure and diversity maintenance in different forest communities.

Niche differentiation and expansion of plant species are associated with mycorrhizal symbiosis

Abstract Mycorrhizal symbiosis is a widespread association between plant roots and mycorrhizal fungi, which is thought to contribute to plant niche differentiation and expansion. However, this has so far not been explicitly tested. To address the effect of mycorrhizal symbiosis on plants’ realized niches, we addressed how mycorrhizal status (i.e. the frequency of occurrence of mycorrhizal symbiosis), flexibility (i.e. the ability to grow both with and without mycorrhizal symbiosis) and type of a plant species affect the realized niche optima, widths and volumes. For this, we used co‐occurrence data from the flora of the Netherlands along soil fertility, moisture, pH, salinity, light and temperature gradients. Phylogenetic dependency of the species was taken into account using phylogenetic generalized least squares models. We show that facultatively and flexibly mycorrhizal plants have the widest niches compared to non‐mycorrhizal and obligately mycorrhizal, and inflexible plants respectively. Among obligate plant symbionts, ecto‐ and ericoid mycorrhizal plants exhibited the widest niches compared to plants with other mycorrhizal types. Also, plants with different mycorrhizal statuses and types differed in their realized niche optima. Synthesis. Our results indicate that mycorrhizal symbiosis mediates plant niche differentiation and expansion, facilitating the understanding of current distribution patterns of plant species, as well as predicting shifts in plant distribution and dominance due to environmental changes.

Evolutionary differences in Δ13C detected between spore and seed bearing plants following exposure to a range of atmospheric O2:CO2 ratios; implications for paleoatmosphere reconstruction

The stable carbon isotopes of fossil plants are a reflection of the atmosphere and environment in which they grew. Fossil plant remains have thus stored information about the isotopic composition and concentration of atmospheric carbon dioxide (pCO2) and possibly pO2 through time. Studies to date, utilizing extant plants, have linked changes in plant stable carbon isotopes (δ13Cp) or carbon isotope discrimination (Δ13C) to changes in pCO2 and/or pO2. These studies have relied heavily on angiosperm representatives, a phylogenetic group only present in the fossil record post-Early Cretaceous (∼140million years ago (mya)), whereas gymnosperms, monilophytes and lycophytes dominated terrestrial ecosystems prior to this time. The aim of this study was to expand our understanding of carbon isotope discrimination in all vascular plant groups of C3 plants including lycophytes, monilophytes, gymnosperms and angiosperms, under elevated CO2 and sub-ambient O2 to explore their utility as paleo-atmospheric proxies. To achieve this goal, plants were grown in controlled environment chambers under a range of O2:CO2 ratio treatments. Results reveal a strong phylogenetic dependency on Δ13C, where spore-bearing (lycophytes and monilophytes) have significantly higher 13C discrimination than seed plants (gymnosperms and angiosperms) by ∼5‰. We attribute this strong phylogenetic signal to differences in Ci/Ca likely mediated by fundamental differences in how spore and seed bearing plants control stomatal aperture. Decreasing O2:CO2 ratio in general resulted in increased carbon isotope discrimination in all plant groups. Notably, while all plant groups respond unidirectionally to elevated atmospheric CO2 (1900ppm and ambient O2), they do not respond equally to sub-ambient O2 (16%). We conclude that (1) Δ13C has a strong phylogenetic or ‘reproductive grade’ bias, whereby Δ13C of spore reproducing plants is significantly different to seed reproducing taxa. (2) Δ13C increases with decreasing O2:CO2 ratios (where significant) but is more likely a result of mechanistically uncoupled responses to elevated pCO2 and sub-ambient O2; and (3) due to this response we find δ13Ca cannot be calculated from δ13Cp unless environmental influences such as O2:CO2 ratio can be independently constrained. Therefore, interpretations of trends in fossil plant δ13Cp to reconstruct paleoatmospheric CO2 concentration should include cross calibration based on a nearest living relative, appropriate nearest living equivalent, or utilizing the phylogenetic corrections produced from this study.

Effects of local biotic neighbors and habitat heterogeneity on seedling survival in a spruce-fir valley forest, northeastern China.

Seedlings are vulnerable to many biotic and abiotic agents, and studying seedling dynamics helps understand mechanisms of species coexistence. In this study, the relative importance of biotic neighbors and habitat heterogeneity to seedling survival was examined by generalized linear mixed models for 33 species in a spruce‐fir valley forest in northeastern China. The results showed that the relative importance of these factors varied with species and functional groups. Conspecific negative density dependence (CNDD) was important to the survival of Abies nephrolepis and Picea koraiensis seedling, whereas phylogenetic negative density dependence (PNDD) was critical to Pinus koraiensis and Betula platyphylla, as well as functional groups of tree, deciduous, and shade‐intolerant seedlings. For shrubs and Acer ukurunduense, habitat heterogeneity was significant. Despite of the significance of CNDD, PNDD, and habitat heterogeneity on seedling survival, large proportions of the total variance were not accounted for by the studied variables, suggesting the needs to examine the influences of other factors such as pests, diseases, herbivores, forest structure, species functional traits, and microclimatic conditions on seedling survival in the future.

Combining phylogenetic footprinting with motif models incorporating intra-motif dependencies

BackgroundTranscriptional gene regulation is a fundamental process in nature, and the experimental and computational investigation of DNA binding motifs and their binding sites is a prerequisite for elucidating this process. Approaches for de-novo motif discovery can be subdivided in phylogenetic footprinting that takes into account phylogenetic dependencies in aligned sequences of more than one species and non-phylogenetic approaches based on sequences from only one species that typically take into account intra-motif dependencies. It has been shown that modeling (i) phylogenetic dependencies as well as (ii) intra-motif dependencies separately improves de-novo motif discovery, but there is no approach capable of modeling both (i) and (ii) simultaneously.ResultsHere, we present an approach for de-novo motif discovery that combines phylogenetic footprinting with motif models capable of taking into account intra-motif dependencies. We study the degree of intra-motif dependencies inferred by this approach from ChIP-seq data of 35 transcription factors. We find that significant intra-motif dependencies of orders 1 and 2 are present in all 35 datasets and that intra-motif dependencies of order 2 are typically stronger than those of order 1. We also find that the presented approach improves the classification performance of phylogenetic footprinting in all 35 datasets and that incorporating intra-motif dependencies of order 2 yields a higher classification performance than incorporating such dependencies of only order 1.ConclusionCombining phylogenetic footprinting with motif models incorporating intra-motif dependencies leads to an improved performance in the classification of transcription factor binding sites. This may advance our understanding of transcriptional gene regulation and its evolution.

Intraspecific and phylogenetic density-dependent seedling recruitment in a subtropical evergreen forest.

Recent evidence suggests that plant performance can be influenced by the phylogenetic diversity of neighboring plants. However, no study to date has examined the effect of such phylogenetic density dependence on the transition from seed to seedling. Using 6years of data on seedling recruitment and seed rain of 13 species from 130 stations (one 0.5m2 seed trap and three adjacent 1m2 seedling plots) in a subtropical evergreen forest, we asked: (1) Does negative density dependence act across seed to seedling stages? (2) Is there evidence for phylogenetic density dependence during the seed to seedling transition? (3) Does the strength of density dependence vary among years? Generalized linear mixed-effects models were used to model seed to seedling transition as a function of conspecific seed and seedling densities, heterospecific seed and seedling densities, and mean phylogenetic distance of heterospecific seeds and seedling. Conspecific seed density had a significant negative effect on seedling transition rates for 12 of 13 focal species. In contrast, conspecific seedling density had a positive effect for 7 species, suggesting species-specific habitat preferences. Few species were significantly affected by the density or phylogenetic relatedness of heterospecific seeds and seedlings. Only conspecific seed density effects varied among years for most focal species. Overall, our results reveal that conspecific seed and seedling densities play a more important role than the density or relatedness of heterospecific seeds and seedlings during the seed to seedling stage, suggesting that species-specific seed predators, along with habitat preferences, may contribute to diversity maintenance in this forest.

Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza

Influenza is responsible for up to 500,000 deaths every year, and antigenic variability represents much of its epidemiological burden. To visualize antigenic differences across many viral strains, antigenic cartography methods use multidimensional scaling on binding assay data to map influenza antigenicity onto a low-dimensional space. Analysis of such assay data ideally leads to natural clustering of influenza strains of similar antigenicity that correlate with sequence evolution. To understand the dynamics of these antigenic groups, we present a framework that jointly models genetic and antigenic evolution by combining multidimensional scaling of binding assay data, Bayesian phylogenetic machinery and nonparametric clustering methods. We propose a phylogenetic Chinese restaurant process that extends the current process to incorporate the phylogenetic dependency structure between strains in the modeling of antigenic clusters. With this method, we are able to use the genetic information to better understand the evolution of antigenicity throughout epidemics, as shown in applications of this model to H1N1 influenza. Copyright © 2017 John Wiley & Sons, Ltd.

Application of Taxonomic Modeling to Microbiota Data Mining for Detection of Helminth Infection in Global Populations.

Human microbiome data from genomic sequencing technologies is fast accumulating, giving us insights into bacterial taxa that contribute to health and disease. The predictive modeling of such microbiota count data for the classification of human infection from parasitic worms, such as helminths, can help in the detection and management across global populations. Real-world datasets of microbiome experiments are typically sparse, containing hundreds of measurements for bacterial species, of which only a few are detected in the bio-specimens that are analyzed. This feature of microbiome data produces the challenge of needing more observations for accurate predictive modeling and has been dealt with previously, using different methods of feature reduction. To our knowledge, integrative methods, such as transfer learning, have not yet been explored in the microbiome domain as a way to deal with data sparsity by incorporating knowledge of different but related datasets. One way of incorporating this knowledge is by using a meaningful mapping among features of these datasets. In this paper, we claim that this mapping would exist among members of each individual cluster, grouped based on phylogenetic dependency among taxa and their association to the phenotype. We validate our claim by showing that models incorporating associations in such a grouped feature space result in no performance deterioration for the given classification task. In this paper, we test our hypothesis by using classification models that detect helminth infection in microbiota of human fecal samples obtained from Indonesia and Liberia countries. In our experiments, we first learn binary classifiers for helminth infection detection by using Naive Bayes, Support Vector Machines, Multilayer Perceptrons, and Random Forest methods. In the next step, we add taxonomic modeling by using the SMART-scan module to group the data, and learn classifiers using the same four methods, to test the validity of the achieved groupings. We observed a 6% to 23% and 7% to 26% performance improvement based on the Area Under the receiver operating characteristic (ROC) Curve (AUC) and Balanced Accuracy (Bacc) measures, respectively, over 10 runs of 10-fold cross-validation. These results show that using phylogenetic dependency for grouping our microbiota data actually results in a noticeable improvement in classification performance for helminth infection detection. These promising results from this feasibility study demonstrate that methods such as SMART-scan can be utilized in the future for knowledge transfer from different but related microbiome datasets by phylogenetically-related functional mapping, to enable novel integrative biomarker discovery.

Influence of cladogenesis on feeding structures in drums (Teleostei: Sciaenidae)

Drums (family Sciaenidae) are common in tropical to temperate coastal and estuarine habitats worldwide and present a broad spectrum of morphological diversity. The anatomical variation in this family is particularly evident in their feeding apparatus, which may reflect the partitioning of adult foraging habitats. Adult and early life history stage sciaenids may display ecomorphological patterns in oral and pharyngeal jaw elements but because sciaenids are hierarchically related, the morphological variation of the feeding apparatus cannot be analyzed as independent data. Morphological patterns have been identified in three sciaenid genera from the Chesapeake Bay but it is not known if these patterns are present in other genera of the family and if such patterns are constrained by phylogenetic history. In this study, phylogenetic comparative methods were applied to two sets of oral jaw data obtained from growth series of 11 species of cleared and double-stained Chesapeake Bay sciaenids and alcohol-preserved museum specimens representing 65 of the 66 recognized genera to determine the magnitude of phylogenetic dependence present in the structure of the oral jaws using a recent molecular phylogeny of the family. Pagel’s lambda, a measure of phylogenetic signal, was low for pelagic sciaenids in premaxilla, lower jaw, and ascending process lengths, indicating influence of selective forces on the condition of these traits. Conversely, for benthic sciaenids, phylogenetic signal was high for lower jaw and ascending process lengths, indicating significant phylogenetic constraint for their condition in these taxa. Pagel’s lambda was intermediate for premaxilla length in benthic sciaenids, suggesting that the length of the premaxilla is influenced by a mix of selective forces and phylogenetic constraint. Although the ecomorphological patterns identified in the oral jaws of scaienids are not entirely free of phylogenetic dependence, selective forces related to foraging are likely driving the evolution of these structures.

Phylogenetic context determines the role of competition in adaptive radiation.

Understanding ecological mechanisms regulating the evolution of biodiversity is of much interest to ecologists and evolutionary biologists. Adaptive radiation constitutes an important evolutionary process that generates biodiversity. Competition has long been thought to influence adaptive radiation, but the directionality of its effect and associated mechanisms remain ambiguous. Here, we report a rigorous experimental test of the role of competition on adaptive radiation using the rapidly evolving bacterium Pseudomonas fluorescens SBW25 interacting with multiple bacterial species that differed in their phylogenetic distance to the diversifying bacterium. We showed that the inhibitive effect of competitors on the adaptive radiation of P. fluorescens decreased as their phylogenetic distance increased. To explain this phylogenetic dependency of adaptive radiation, we linked the phylogenetic distance between P. fluorescens and its competitors to their niche and competitive fitness differences. Competitive fitness differences, which showed weak phylogenetic signal, reduced P. fluorescens abundance and thus diversification, whereas phylogenetically conserved niche differences promoted diversification. These results demonstrate the context dependency of competitive effects on adaptive radiation, and highlight the importance of past evolutionary history for ongoing evolutionary processes.

Global patterns of mammalian co‐occurrence: phylogenetic and body size structure within species ranges

AbstractAimTo analyse the geographical co‐occurrence among mammal species based on their complete geographical distributions, considering their phylogenetic relationships and body size data. We describe species‐level patterns and test the relative effects of ecological and evolutionary processes in determining species co‐occurrence under the phylogenetic field framework.LocationGlobal.MethodsWe gathered distributional, phylogenetic and body size information for 3697 mammal species. We defined phylogenetic fields of species by estimating the phylogenetic structure of species co‐occurrence within a focal species' range. Likewise, body size structure within focal species' ranges was defined as body size fields. We applied a spatial‐phylogenetic statistical framework to evaluate geographical variation on species fields. Also, we tested the significance of phylogenetic and body size fields based on biogeographically informed null models. Analyses were done for all mammal species as a whole and within particular taxonomic orders.ResultsPhylogenetic and body size fields of mammal species showed significant geographical patterning beyond their spatial and phylogenetic dependence. Phylogenetic fields were strikingly different between the New and Old World, with mammals co‐occurring with more closely related species in the New World and more distantly related species in the Old World. Clustered phylogenetic and body size fields showed geographically congruent patterns. Similar findings were obtained within particular mammalian orders.Main conclusionsGeographical co‐occurrence among mammal species reveals the imprint of historical origins and dispersal of mammalian lineages. Phylogenetic and body size structure within mammalian ranges is driven by the distinct histories among biogeographical regions and mainly between the New and Old World. We demonstrate the usefulness of a new protocol integrating species' distributional, phylogenetic and body size information for linking evolutionary and ecological approaches to understand geographical patterns of biodiversity.

How does habitat filtering affect the detection of conspecific and phylogenetic density dependence?

Conspecific negative density dependence (CNDD) has been recognized as a key mechanism underlying species coexistence, especially in tropical forests. Recently, some studies have reported that seedling survival is also negatively correlated with the phylogenetic relatedness between neighbors and focal individuals, termed phylogenetic negative density dependence (PNDD). In contrast to CNDD or PNDD, shared habitat requirements between closely related individuals are thought to be a cause of observed positive effects of closely related neighbors, which may affect the strength and detectability of CNDD or PNDD. In order to investigate the relative importance of these mechanisms for tropical tree seedling survival, we used generalized linear mixed models to analyze how the survival of more than 10 000 seedlings of woody plant species related to neighborhood and habitat variables in a tropical rainforest in southwest China. By comparing models with and without habitat variables, we tested how habitat filtering affected the detection of CNDD and PNDD. The best-fitting model suggested that CNDD and habitat filtering played key roles in seedling survival; but that, contrary to our expectations, phylogenetic positive density dependence (PPDD) had a distinct and important effect. While habitat filtering affected the detection of CNDD by decreasing its apparent strength, it did not explain the positive effects of closely related neighbors. Our results demonstrate that a failure to control for habitat variables and phylogenetic relationships may obscure the importance of conspecific and heterospecific neighbor densities for seedling survival.

Szidat's rule re-tested: relationships between flea and host phylogenetic clade ranks in four biogeographic realms.

We tested Szidat's rule (the more primitive the host, the more primitive the parasites it harbours) by analysing the relationships between phylogenetic clade ranks of fleas and their small mammalian hosts in four biogeographic realms (Afrotropics, Neotropics, Nearctic and Palearctic). From the host perspective, we tested the association between host clade rank and the mean clade rank of all fleas collected from this host. From the flea perspective, we tested the relationships between flea clade rank and the mean clade rank of hosts on which this flea was recorded. First, we tested whether the analysis of the relationships between host and flea clade ranks should be controlled for phylogenetic dependence among either host or flea species. Then, we tested for the associations between host and flea clade ranks separately for each realm using either a phylogenetic general least-squares analysis or an ordinary least-squares analysis. In all realms, the mean clade rank of fleas parasitic on a given host increased with an increase of this host's clade rank, and the mean clade rank of hosts recorded on a given flea increased with an increase of this flea's clade rank, suggesting that Szidat's rule, at least to some extent, holds for fleas.