Phylogenetic Models Research Articles

Genome-wide evolutionary analysis of AUX/IAA gene family in wheat identifies a novel gene TaIAA15-1A regulating flowering time by interacting with ARF

Flowering time is a critical agronomic trait that has strong effects on crop yields. Auxin signaling pathway plays an important role in various development processes, such as flowering, grain development. However, no Aux/IAA gene had been reported to have functions involving in wheat flowering time. Here, we systematically performed genome-wide identification, classification, domain distribution, exon-intron structure, chromosome locations and global expression pattern of Aux/IAA gene family in 14 plant genomes (including Triticum aestivum). A phylogenetic model was proposed to infer the Aux/IAA evolutionary history involving in a central exon-intron structure “2121” during evolution. Overexpression of TaIAA15-1A caused an early flowering time in Brachypodium. RNA-seq analysis showed that TaIAA15-1A overexpression alters various pathways including phytohormone signaling pathway, flowering-related pathway, and polyamine biosynthesis pathway. Screening of auxin response factor (ARF) genes identified BdARF16 that interacted with TaIAA15-1A. Exogenous polyamine (spermidine and spermine) treatments promoted early flowering and (putrescine and DCHA) delayed flowering time of WT plants. Our finding will provide insights on mechanisms of Aux/IAAs gene family and TaIAA15-1A, illustrating the potential during crop improvement programs.

Environment‐dependent influence of fruit size upon the distribution of the Malesian archipelagic flora

Societal Impact StatementWe found evidence that larger fruited plant species are more likely to be found in aseasonal wet areas of Malesia. These areas are likely to be impacted by increasing human encroachment, which threatens both large‐fruited species and the large fauna that are most likely responsible for their dispersal. This synergistic threat could drive the loss of fruit‐crop relatives that potentially have key traits for resilient fruit crops of the future.Summary It is unclear how fruit size determines distributions of megadiverse tropical flora. Energetic constraints of ecosystems suggest plant species with larger fruit should be found in the higher productivity, aseasonal wet tropics. However, the probability of seed dispersal over large scales should be increased by fruits being smaller, due to being available to a greater number of dispersal agents. We use a Bayesian phylogenetic model of species occurrence for >3400 species in Malesia to test how fruit size and environment interact to determine species distributions across the archipelago. We show that larger fruited species are more likely to occur in aseasonal wet areas. We also found that smaller fruit size was associated with species occurrence in more mountainous areas. Fruit size interacts with environmental variables to shape plant distributions across the megadiverse Malesian islands. The evolutionary processes that influence the patterns we have observed require further examination.

Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates.

Human immunodeficiency virus 1 (HIV-1) is a rapidly evolving virus able to evade host immunity through rapid adaptation during chronic infection. The HIV-1 group M has diversified since its zoonosis into several subtypes at a rate of the order of 10-3 changes per site per year. This rate varies between different parts of the genome, and its inference is sensitive to the timescale and diversity spanned by the sequence data used. Higher rates are estimated on short timescales and particularly for within-host evolution, while rate estimates spanning decades or the entire HIV-1 pandemic tend to be lower. The underlying causes of this difference are not well understood. We investigate here the role of rapid reversions toward a preferred evolutionary sequence state on multiple timescales. We show that within-host reversion mutations are under positive selection and contribute substantially to sequence turnover, especially at conserved sites. We then use the rates of reversions and non-reversions estimated from longitudinal within-host data to parameterize a phylogenetic sequence evolution model. Sequence simulation of this model on HIV-1 phylogenies reproduces diversity and apparent evolutionary rates of HIV-1 in gag and pol, suggesting that a tendency to rapidly revert to a consensus-like state can explain much of the time dependence of evolutionary rate estimates in HIV-1.

The anti-inflammatory cytokine IL-22 exhibited a proinflammatory effect in the ovary aiding with the parturition of ovoviviparous black rockfish (Sebastes schlegelii)

IntroductionAs a unique type of immunological process, pregnancy and subsequent parturition are associated with a series of inflammatory events. As an anti-inflammatory cytokine, IL-22 has been proven to participate in the parturition process in mammals. However, less is known about ovoviviparous teleosts. To investigate the role of IL-22 in fish parturition, black rockfish, an ovoviviparous teleost, was used. This fish is unique in that it provides over 60% nutrition supply for over 50 thousand embryos at the same time though a placenta-like structure during pregnancy while delivering all fries in two hours.MethodsSequence alignment, phylogenetic tree analysis and homology modeling were performed on IL-22 and its receptor. In situ hybridization demonstrated ovarian localization of il22 and il22r1. The protein of rIL-22 was obtained through the prokaryotic expression. RNA-seq analysis was performed on black rockfish ovarian cells treated with rIL-22.ResultsIn situ hybridization results showed that both il22 and il22ra1 were localized in the perinatal follicle layer and embryonic envelope. The il22 expression level was significantly increased during parturition compared to before and after parturition (P<0.05). To further understand the mechanism of IL-22 in parturition, rIL-22 was obtained. The downstream variation genes in primary cultured ovarian cells in the perinatal period were analyzed according to the transcriptomic results. A total of 168 differentially expressed genes (DEGs) were identified in the rIL-22 group compared with the PBS control group (padj < 0.05 and |log2FoldChange| 1). Of those, 134 DEGs were identified in the LPS and rIL-22 treatment groups, including chemokine, cytokine, and PG synthesis. 34 DEGs were mainly identified in immune-related pathways and reorganization of the cytoskeleton responded only to rIL-22 stimulation but not LPS. KEGG pathways mainly included immune response, PG synthesis, cell death and angiogenesis (p value < 0.05).DiscussionTaken together, our results indicated that IL-22 plays an important role in the parturition of black rockfish by upregulating PG synthesis and increasing chemokine, proinflammatory factor, as well as PG synthetase levels.

A quantitative global test of the complexity trade-off hypothesis: the case of nominal and verbal grammatical marking

AbstractNouns and verbs are known to differ in the types of grammatical information they encode. What is less well known is the relationship between verbal and nominal coding within and across languages. The equi-complexity hypothesis holds that all languages are equally complex overall, which entails trade-offs between coding in different domains. From a diachronic point of view, this hypothesis implies that the loss and gain of coding in different domains can be expected to balance each other out. In this study, we test to what extent such inverse coevolution can be observed in a sample of 244 languages, using data from a comprehensive cross-linguistic database (Grambank) and applying computational phylogenetic modelling to control for genealogical relatedness. We find evidence for coevolutionary relationships between specific features within nominal and verbal domains on a global scale, but not for overall degrees of grammatical coding between languages. Instead, these amounts of nominal and verbal coding are positively correlated in Sino-Tibetan languages and inversely correlated in Indo-European languages. Our findings indicate that accretion and loss of grammatical information in nominal words and verbs are lineage-specific.

Functional traits mediate individualistic species-environment distributions at broad spatial scales while fine-scale species associations remain unpredictable.

Numerous processes influence plant distributions and co-occurrence patterns, including ecological sorting, limiting similarity, and stochastic effects. To discriminate among these processes and determine the spatial scales at which they operate, we investigated how functional traits and phylogenetic relatedness influence the distribution of temperate forest herbs. We surveyed understory plant communities across 257 forest stands in Wisconsin and Michigan (USA) and applied Bayesian phylogenetic linear mixed-effects models (PGLMMs) to quantify how functional traits and phylogenetic relatedness influence the environmental distribution of 139 herbaceous plant species along broad edaphic, climatic, and light gradients. These models also allowed us to test how functional and phylogenetic similarity affect species co-occurrence within microsites. Leaf height, specific leaf area, and seed mass all influenced individualistic plant distributions along landscape-scale gradients in soil texture, soil fertility, light availability, and climate. In contrast, phylogenetic relationships did not consistently predict species-environment relationships. Neither functionally similar nor phylogenetically related herbs segregated among microsites within forest stands. Trait-mediated ecological sorting appears to drive temperate-forest community assembly, generating individualistic plant distributions along regional environmental gradients. This finding links classic studies in plant ecology and prior research in plant physiological ecology to current trait-based approaches in community ecology. However, our results fail to support the common assumption that limiting similarity governs local plant co-occurrences. Strong ecological sorting among forest stands coupled with stochastic fine-scale interactions among species appear to weaken deterministic, niche-based assembly processes at local scales.

Two results about the Sackin and Colless indices for phylogenetic trees and their shapes.

The Sackin and Colless indices are two widely-used metrics for measuring the balance of trees and for testing evolutionary models in phylogenetics. This short paper contributes two results about the Sackin and Colless indices of trees. One result is the asymptotic analysis of the expected Sackin and Colless indices of tree shapes (which are full binary rooted unlabelled trees) under the uniform model where tree shapes are sampled with equal probability. Another is a short direct proof of the closed formula for the expected Sackin index of phylogenetic trees (which are full binary rooted trees with leaves being labelled with taxa) under the uniform model.

Climate change will redefine taxonomic, functional, and phylogenetic diversity of Odonata in space and time

Climate change is rearranging the mosaic of biodiversity worldwide. These broad-scale species re-distributions affect the structure and composition of communities with a ripple effect on multiple biodiversity facets. Using European Odonata, we asked: i) how climate change will redefine taxonomic, phylogenetic, and functional diversity at European scales; ii) which traits will mediate species’ response to global change; iii) whether this response will be phylogenetically conserved. Using stacked species distribution models, we forecast widespread latitudinal and altitudinal rearrangements in Odonata community composition determining broad turnovers in traits and evolutionary lineages. According to our phylogenetic regression models, only body size and flight period can be partly correlated with observed range shifts. In considering all primary facets of biodiversity, our results support the design of inclusive conservation strategies able to account for the diversity of species, the ecosystem services they provide, and the phylogenetic heritage they carry in a target ecosystem.

Effect of Polytomy on the Parameter Estimation and Goodness of Fit of Phylogenetic Linear Regression Models for Trait Evolution

Phylogenetic regression models for trait evolution incorporate phylogenetic trees for the analysis of comparative data, in order to study trait relationships among a group of related species. However, as such trees are estimated, it is unlikely that there will be no errors when describing the relationships among species. In particular, for polytomy trees, where the relationships within a particular clade of species are more/less certainly determined (hard/soft polytomy, respectively), results of comparative analyses obtained from models based on those phylogenetic trees may also be affected. In this study, through extensive simulations, the performances of several popular Gaussian process-based regression models (Brownian motion, BM; Ornstein–Uhlenbeck process, OU; early burst, EB), as well as branch-stretching models (Pagel’s λ,δ,κ), were evaluated by assessing their fit and parameter estimation performance when soft polytomies are presented on either the root or a clade with insufficient phylogenetic information. Comparisons of the models are conducted by either assessing the accuracy of the estimator of regression and model parameters, or using a measure of fit (AIC, r2, and mean square error). It is found that, although polytomy does not significantly impact the fit and parameter estimate within a specified model, distinguishable differences and effects may be observed among trees and models. In particular, Pagel λ model and the OU model yield more accurate estimates and provide better fitting effects than the other models (BM, EB, δ, κ). While correcting phylogeny is an essential step prior to analysis, users may also consider using more appropriate models when encountering the polytomy issue.

Complex statistical modelling for phylogenetic inference

AbstractMolecular sequence data are a primary source of information about evolutionary relationships. Over the past few decades, there have been dramatic increases in the sizes of data available. Consequently, focus has shifted towards increasingly complex models that are less prone to the biases that are a consequence of model misspecification. At the same time, the computational challenges, which were always substantial, have become greater due to these increasingly complex models and larger data sizes. In this article, we review phylogenetic inference using sequence data and some recent advances in phylogenetic modelling. We discuss strategies for dealing with complex models, future challenges and paths forward.

Phylogeny explains capture mortality of sharks and rays in pelagic longline fisheries: a global meta-analytic synthesis

Apex and mesopredators such as elasmobranchs are important for maintaining ocean health and are the focus of conservation efforts to mitigate exposure to fishing and other anthropogenic hazards. Quantifying fishing mortality components such as at-vessel mortality (AVM) is necessary for effective bycatch management. We assembled a database for 61 elasmobranch species and conducted a global meta-synthesis to estimate pelagic longline AVM rates. Evolutionary history was a significant predictor of AVM, accounting for up to 13% of variance in Bayesian phylogenetic meta-regression models for Lamniformes and Carcharhiniformes clades. Phylogenetically related species may have a high degree of shared traits that explain AVM. Model-estimated posterior mean AVM rates ranged from 5% (95% HDI 0.1%–16%) for pelagic stingrays and 76% (95% HDI 49%–90%) for salmon sharks. Measures that reduce catch, and hence AVM levels, such as input controls, bycatch quotas and gear technology to increase selectivity are appropriate for species with higher AVM rates. In addition to reducing catchability, handling-and-release practices and interventions such as retention bans in shark sanctuaries and bans on shark finning and trade hold promise for species with lower AVM rates. Robust, and where applicable, phylogenetically-adjusted elasmobranch AVM rates are essential for evidence-informed bycatch policy.

The evolution of marsupial social organization.

It is generally believed that marsupials are more primitive than placentals mammals and mainly solitary living, representing the ancestral form of social organization of all mammals. However, field studies have observed pair and group-living in marsupial species, but no comparative study about their social evolution was ever done. Here, we describe the results of primary literature research on marsupial social organization which indicates that most species can live in pairs or groups and many show intra-specific variation in social organization. Using Bayesian phylogenetic mixed-effects models with a weak phylogenetic signal of 0.18, we found that solitary living was the most likely ancestral form (35% posterior probability), but had high uncertainty, and the combined probability of a partly sociable marsupial ancestor (65%) should not be overlooked. For Australian marsupials, group-living species were less likely to be found in tropical rainforest, and species with a variable social organization were associated with low and unpredictable precipitation representing deserts. Our results suggest that modern marsupials are more sociable than previously believed and that there is no strong support that their ancestral state was strictly solitary living, such that the assumption of a solitary ancestral state of all mammals may also need reconsideration.

Plant species biogeographic origin shapes their current and future distribution on the world's highest island mountain

Abstract In New Guinea, low elevations are thought to be dominated by plant species with biogeographic origins in Sunda (Borneo, Sumatra, Java, Mainland Asia) and high elevations by species from Sahul (Australia and New Guinea). In regions where frequent surveys of the flora are unfeasible, herbarium specimens collected over time offer an opportunity to study the co‐occurrence of species. Over 7000 collections have been made on New Guinea's Mount Jaya allowing us to examine species presence under current and future temperatures. Applying a Bayesian phylogenetic mixed effects model to the Mount Jaya elevation gradient, we show that species of Sunda origin are more likely to occupy warmer lowlands and Sahul species cooler higher elevations. Using the model to predict species distributions under a 2°C increase, we find that Sahul species are less likely to tolerate future temperatures, especially below 1000 m. Predictions also show a potential increase in species richness across the gradient. It is unclear if these increases are possible due to limits imposed by the species area relationship. Synthesis. These results emphasise how biogeographic origin influences current and future species distributions on tropical mountains. It remains to be seen how our results link to traits that dictate species' ability to tolerate increasing temperatures.

A Timeframe for SARS-CoV-2 Genomes: A Proof of Concept for Postmortem Interval Estimations.

Establishing the timeframe when a particular virus was circulating in a population could be useful in several areas of biomedical research, including microbiology and legal medicine. Using simulations, we demonstrate that the circulation timeframe of an unknown SARS-CoV-2 genome in a population (hereafter, estimated time of a queried genome [QG]; tE-QG) can be easily predicted using a phylogenetic model based on a robust reference genome database of the virus, and information on their sampling dates. We evaluate several phylogeny-based approaches, including modeling evolutionary (substitution) rates of the SARS-CoV-2 genome (~10-3 substitutions/nucleotide/year) and the mutational (substitutions) differences separating the QGs from the reference genomes (RGs) in the database. Owing to the mutational characteristics of the virus, the present Viral Molecular Clock Dating (VMCD) method covers timeframes going backwards from about a month in the past. The method has very low errors associated to the tE-QG estimates and narrow intervals of tE-QG, both ranging from a few days to a few weeks regardless of the mathematical model used. The SARS-CoV-2 model represents a proof of concept that can be extrapolated to any other microorganism, provided that a robust genome sequence database is available. Besides obvious applications in epidemiology and microbiology investigations, there are several contexts in forensic casework where estimating tE-QG could be useful, including estimation of the postmortem intervals (PMI) and the dating of samples stored in hospital settings.

The robustness of a simple dynamic model of island biodiversity to geological and sea‐level change

AbstractAimBiodiversity on islands is influenced by geophysical processes and sea‐level fluctuations. Oceanic islands (never connected to a landmass) are initially vacant with diversity accumulating via colonisation and speciation, and then declining as islands shrink. Continental islands have species upon disconnection from the mainland and may have transient land‐bridge connections. Theoretical predictions for the effects of these geophysical processes on rates of colonisation, speciation, and extinction have been proposed. However, paleogeographic reconstructions are currently unavailable for most islands, and phylogenetic models overlook island ontogeny, sea‐level changes, or past landmass connections. We analyse to what extent ignoring geodynamics in the inference model affects model predictions when confronted with data simulated with geodynamics.LocationSimulations of oceanic and continental islands.TaxaSimulated lineages.MethodsWe extend the island biogeography simulation model DAISIE to include: (i) area‐dependent rates of colonisation and diversification associated with island ontogeny and sea‐level fluctuations, (ii) continental islands with biota present upon separation from the mainland, and (iii) shifts in colonisation to mimic temporary land‐bridges. We quantify the error of ignoring geodynamic processes by applying DAISIE's inference method to geodynamic simulations.ResultsRobustness of the model to dynamic island area is generally high for oceanic islands and for continental islands that have been separated for a long time, suggesting that it is possible to obtain reliable results when ignoring geodynamics. However, for continental islands that have been recently or frequently connected, robustness of the model is low.Main conclusionsUnder many island biogeographic geodynamic scenarios (oceanic islands and ancient continental fragments) a simple phylogenetic model ignoring geodynamics is empirically applicable and informative. However, recent connection to the continent cannot be ignored, requiring new model development. Our results show that for oceanic islands, reliable insights can be obtained from phylogenetic data in the absence of paleogeographic reconstructions of island area.

Parallel evolution of semicircular canal form and sensitivity in subterranean mammals.

The vertebrate vestibular system is crucial for balance and navigation, and the evolution of its form and function in relation to species' lifestyle and mode of locomotion has been the focus of considerable recent study. Most research, however, has concentrated on aboveground mammals, with much less published on subterranean fauna. Here, we explored variation in anatomy and sensitivity of the semicircular canals among 91 mammal species, including both subterranean and non-subterranean representatives. Quantitative phylogenetically informed analyses showed significant widening of the canals relative to radius of curvature in subterranean species. A relative canal width above 0.166 indicates with 95% certainty that a species is subterranean. Fluid-structure interaction modelling predicted that canal widening leads to a substantial increase in canal sensitivity; a reasonably good estimation of the absolute sensitivity is possible based on the absolute internal canal width alone. In addition, phylogenetic comparative modelling and functional landscape exploration revealed repeated independent evolution of increased relative canal width and anterior canal sensitivity associated with the transition to a subterranean lifestyle, providing evidence of parallel adaptation. Our results suggest that living in dark, subterranean tunnels requires good balance and/or navigation skills which may be facilitated by more sensitive semicircular canals.

Seasonal variation significantly influenced the stochasticity of community assembly of amphibian symbiotic bacteria.

Seasonal variation has been shown to influence symbiotic bacterial community composition and structure in amphibians. It is still unknown how the symbiotic bacterial community assembly changes during different seasons, especially for amphibians who are particularly sensitive to environmental change. We found significant differences in the composition and diversity (alpha and beta diversity) of amphibian skin and gut bacteria. Co-occurrences network analysis showed that seasonal variation reduced the microbial network complexity of amphibians from summer to autumn. The normalized stochastic ratio (NST) and phylogenetic bin-based null model analysis (iCAMP) models showed that the same result that stochastic processes was the major factor regulating the symbiotic bacterial community assembly mechanisms of amphibians. From summer to autumn, the symbiotic bacterial community assembly mechanisms declined in the contribution of stochastic processes, while increasing in the contribution of deterministic processes. Dispersal limitation was the dominant microbial assembly mechanism, followed by homogeneous selection, and then heterogeneous selection in the symbiotic bacterial community communities of amphibians between summer and autumn. Furthermore, higher niche width of the symbiotic bacterial community of amphibians was found in summer than autumn. Overall, these results demonstrated that seasonal variation influenced amphibian symbiotic bacterial community between summer and autumn.

Do closely related species interact with similar partners? Testing for phylogenetic signal in bipartite interaction networks

Whether interactions between species are conserved on evolutionary time-scales has spurred the development of both correlative and process-based approaches for testing phylogenetic signal in interspecific interactions: do closely related species interact with similar partners? Here we use simulations to test the statistical performances of the two approaches that are the most widely used in the field: Mantel tests and the Phylogenetic Bipartite Linear Model (PBLM). Mantel tests investigate the correlation between phylogenetic distances and dissimilarities in sets of interacting partners, while PBLM is a process-based approach that relies on strong assumptions about how interactions evolve. We find that PBLM often detects a phylogenetic signal when it should not. Simple Mantel tests instead have infrequent false positives and moderate statistical power; however, they often artifactually detect that closely related species interact with dissimilar partners. Partial Mantel tests, which are used to partial out the phylogenetic signal in the number of partners, actually fail at correcting for this confounding effect, and we instead recommend evaluating the significance of Mantel tests with network permutations constraining the number of partners. We also explore the ability of simple Mantel tests to analyze clade- specific phylogenetic signals. We provide general guidelines and an application on an interaction network between orchids and mycorrhizal fungi.

Correlated evolution between colour conspicuousness and drum speed in woodpeckers.

Sexual selection drives the evolution of many spectacular animal displays that we see in nature. Yet, how selection combines and elaborates different signal traits remains unclear. Here, we investigate this issue by testing for correlated evolution between head plumage colour and drumming behaviour in woodpeckers. These signals function in the context of mate choice and male–male competition, and they may appear to a receiver as a single multimodal display. We test for such correlations in males of 132 species using phylogenetic linear models, while considering the effect of habitat. We find that the plumage chromatic contrast is positively correlated with the speed of the drum, supporting the idea that species evolving more conspicuous plumage on their head also evolve faster drum displays. By contrast, we do not find evidence of correlated evolution between drum speed and head colour diversity, size of the head's red patch, or extent of the plumage achromatic contrast. Drum length was not correlated with any of the plumage coloration metrics. Lastly, we find no evidence that habitat acts as a strong selective force driving the evolution of head coloration or drumming elaboration. Coevolution between different signal modalities is therefore complex, and probably depends on the display components in question.

SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework.

Genomic epidemiology is now widely used for viral outbreak investigations. Still, this methodology faces many challenges. First, few methods account for intra-host viral diversity. Second, maximum parsimony principle continues to be employed for phylogenetic inference of transmission histories, even though maximum likelihood or Bayesian models are usually more consistent. Third, many methods utilize case-specific data, such as sampling times or infection exposure intervals. This impedes study of persistent infections in vulnerable groups, where such information has a limited use. Finally, most methods implicitly assume that transmission events are independent, although common source outbreaks violate this assumption. We propose a maximum likelihood framework, SOPHIE, based on the integration of phylogenetic and random graph models. It infers transmission networks from viral phylogenies and expected properties of inter-host social networks modeled as random graphs with given expected degree distributions. SOPHIE is scalable, accounts for intra-host diversity, and accurately infers transmissions without case-specificepidemiological data.