Phylogenetic Models Research Articles

Проблема направленности филогенеза и биоэнергетический прогресс: новая модель эволюции жизни

In modern biology, the contours of a new idea of the development of life, based on the ideas of the concept of mega-evolution, are being formed. Unlike phylogenetic models created within the framework of micro- and macroevolutionary analysis, the theory of mega-evolution shows us a picture not just of the direction, but of the predestination of the main acts of the development of living things. The article substantiates the position that the predestination of mega-evolution is largely determined by the direction of bioenergetic progress, which in turn is the basis for the growth of the activity of the living and the improvement of the mechanisms of its expedient device. This vector of evolution of the living, formed in the first act of the origin of life as a non-trivial way to overcome energy barriers, determines the development of organic life to this day.

Single-cell resolved ploidy and chromosomal aberrations in nonalcoholic steatohepatitis-(NASH) induced hepatocellular carcinoma and its precursor lesions

Nonalcoholic steatohepatitis (NASH)-induced hepatocellular carcinoma (HCC) and its precursor, nonalcoholic fatty liver disease (NAFLD) are an unmet health issue due to widespread obesity. We assessed copy number changes of genes associated with hepatocarcinogenesis and oxidative pathways at a single-cell level. Eleven patients with NASH-HCC and 11 patients with NAFLD were included. Eight probes were analyzed using multiplex interphase fluorescence in situ hybridization (miFISH), single-cell imaging and phylogenetic tree modelling: Telomerase reverse transcriptase (TERT), C-Myc (MYC), hepatocyte growth factor receptor tyrosine kinase (MET), tumor protein 53 (TP53), cyclin D1 (CCND1), human epidermal growth factor receptor 2 (HER2), the fragile histidine triad gene (FHIT) and FRA16D oxidoreductase (WWOX). Each NASH-HCC tumor had up to 14 distinct clonal signal patterns indicating multiclonality, which correlated with high tumor grade. Changes frequently observed were TP53 losses, 45%; MYC gains, 36%; WWOX losses, 36%; and HER2 gains, 18%. Whole-genome duplications were frequent (82%) with aberrant tetraploid cells evolving from diploid ancestors. Non-tumorous NAFLD/NASH biopsies did not harbor clonal copy number changes. Fine mapping of NASH-HCC using single-cell multiplex FISH shows that branched tumor evolution involves genome duplication and that multiclonality increases with tumor grade. The loss of oxidoreductase WWOX and HER2 gains could be potentially associated with NASH-induced hepatocellular carcinoma.

Performance of Akaike Information Criterion and Bayesian Information Criterion in Selecting Partition Models and Mixture Models.

In molecular phylogenetics, partition models and mixture models provide different approaches to accommodating heterogeneity in genomic sequencing data. Both types of models generally give a superior fit to data than models that assume the process of sequence evolution is homogeneous across sites and lineages. The Akaike Information Criterion (AIC), an estimator of Kullback-Leibler divergence, and the Bayesian Information Criterion (BIC) are popular tools to select models in phylogenetics. Recent work suggests that AIC should not be used for comparing mixture and partition models. In this work, we clarify that this difficulty is not fully explained by AIC misestimating the Kullback-Leibler divergence. We also investigate the performance of the AIC and BIC at comparing amongst mixture models and amongst partition models. We find that under nonstandard conditions (i.e. when some edges have small expected number of changes), AIC underestimates the expected Kullback-Leibler divergence. Under such conditions, AIC preferred the complex mixture models and BIC preferred the simpler mixture models. The mixture models selected by AIC had a better performance in estimating the edge length, while the simpler models selected by BIC performed better in estimating the base frequencies and substitution rate parameters. In contrast, AIC and BIC both prefer simpler partition models over more complex partition models under nonstandard conditions, despite the fact that the more complex partition model was the generating model. We also investigated how mispartitioning (i.e., grouping sites that have not evolved under the same process) affects both the performance of partition models compared with mixture models and the model selection process. We found that as the level of mispartitioning increases, the bias of AIC in estimating the expected Kullback-Leibler divergence remains the same, and the branch lengths and evolutionary parameters estimated by partition models become less accurate. We recommend that researchers are cautious when using AIC and BIC to select among partition and mixture models; other alternatives, such as cross-validation and bootstrapping, should be explored, but may suffer similar limitations [AIC; BIC; mispartitioning; partitioning; partition model; mixture model].

Distributions of cherries and pitchforks for the Ford model

Distributional properties of tree shape statistics under random phylogenetic tree models play an important role in investigating the evolutionary forces underlying the observed phylogenies. In this paper, we study two subtree counting statistics, the number of cherries and that of pitchforks for the Ford model, the alpha model introduced by Daniel Ford. It is a one-parameter family of random phylogenetic tree models which includes the proportional to distinguishable arrangement (PDA) and the Yule models, two tree models commonly used in phylogenetics. Based on a non-uniform version of the extended Pólya urn models in which negative entries are permitted for their replacement matrices, we obtain the strong law of large numbers and the central limit theorem for the joint distribution of these two statistics for the Ford model. Furthermore, we derive a recursive formula for computing the exact joint distribution of these two statistics. This leads to exact formulas for their means and higher order asymptotic expansions of their second moments, which allows us to identify a critical parameter value for the correlation between these two statistics. That is, when the number of tree leaves is sufficiently large, they are negatively correlated for 0≤α≤1/2 and positively correlated for 1/2<α<1.

A critical assessment of ex situ conservation based on the Brazilian avifauna: Are we focusing on what is easier?

Species have been lost at unprecedented rates. Because only a small fraction of the threatened taxa have been managed under human care, contrasting the characteristics of taxa that have, and have not been targeted to ex situ conservation can reveal the reach of this conservation strategy, and can indicate its main challenges. Here we investigated whether the level of threat, diet, body mass, phylogeny, and previous presence in captivity due to non-conservation purposes could be potential parameters accounting for the occurrence of Brazilian threatened avian species and subspecies in ex situ conservation facilities and for their eligibility to organized ex situ conservation plans. Using Bayesian phylogenetic comparative models we found positive effects of body mass and phylogeny, and a negative effect of insectivorous diet in the occurrence of the taxa in non-conservation facilities. The previous presence in non-conservation facilities, together with phylogeny, diet, and body mass were the main parameters accounting for the occurrence of the threatened taxa in ex situ conservation facilities, and the previous presence in non-conservation facilities and phylogeny explained the existence of organized ex situ conservation plans. This is evidence that conservation breeding facilities have mostly harbored threatened confiscated birds than choosing them based on scientific criteria. We suggest that investing in the development of husbandry techniques, especially for insectivorous passerines, and choosing taxa based on scientific criteria are important challenges that should be on the agenda of conservation managers.

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 &gt;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&amp;lt;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 &amp;lt; 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 &amp;lt; 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.