Phylogenetic Models Research Articles

Identifying co-phylogenetic hotspots for zoonotic disease.

The incidence of zoonotic diseases is increasing worldwide, which makes identifying parasites likely to become zoonotic and hosts likely to harbour zoonotic parasites a critical concern. Prior work indicates that there is a higher risk of zoonotic spillover accruing from closely related hosts and from hosts that are infected with a high phylogenetic diversity of parasites. This suggests that host and parasite evolutionary history may be important drivers of spillover, but identifying whether host-parasite associations are more strongly structured by the host, parasite or both requires co-phylogenetic analyses that combine host-parasite association data with host and parasite phylogenies. Here, we use host-parasite datasets containing associations between helminth taxa and free-range mammals in combination with phylogenetic models to explore whether host, parasite, or both host and parasite evolutionary history influences host-parasite associations. We find that host phylogenetic history is most important for driving patterns of helminth-mammal association, indicating that zoonoses are most likely to come from a host's close relatives. More broadly, our results suggest that co-phylogenetic analyses across broad taxonomic scales can provide a novel perspective for surveying potential emerging infectious diseases. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.

Ecological and behavioural drivers of offspring size in marine teleost fishes

AbstractAimOur aim was to evaluate the role of ecological and life‐history factors in shaping global variation in offspring size in a marine clade with a diverse range of parental care behaviours.LocationGlobal.Time periodData sourced from literature published from 1953 until 2019.Major taxa studiedMarine teleost fishes.MethodsWe compiled a species‐level dataset of egg and hatch size for 1,639 species of marine fish across 45 orders. We used Bayesian phylogenetic mixed models to evaluate the relationship between offspring size and environmental factors (i.e., mean temperature, chlorophyll‐a and dissolved oxygen content together with their annual variation), as well as latitude, reproductive strategy, parental body size and fecundity. We also tested long‐standing hypotheses about the co‐evolution of offspring size and the presence of parental care in BayesTraits.ResultsAfter controlling for parental body size and phylogenetic history, we find that increased egg size is associated with colder and oxygen‐rich waters, while hatch size further depends on food supply and the reproductive strategy exhibited by the species. Irrespective of the initial investment in egg size, species with parental care or demersal egg development yield larger hatchlings compared to pelagic spawners. We also demonstrate that hatch size has co‐evolved with advanced forms of care in association with parental body but fail to find a relationship with other types of care.Main conclusionsOur study shows that parental care behaviours, together with environmental context, influence the evolution of classic life‐history trade‐offs on a global scale. While the initial investment in eggs is driven primarily by temperature and oxygen content, hatch size also reflects the impact of care an offspring has received throughout development. In support of the ‘offspring‐first’ hypothesis, we find that an increase in hatch size drives the evolution of advanced care provision.

Genome-wide data reveal extensive gene flow during the diversification of the western rattlesnakes (Viperidae: Crotalinae: Crotalus)

Hybridization and introgression are important, but often overlooked processes when inferring phylogenies. When these processes are not accounted for and a strictly diverging phylogenetic model is applied to groups with a history of hybridization, phylogenetic inference and parameter estimation can be inaccurate. Recent developments in phylogenetic network approaches coupled with the increasing availability of genomic data allow inferences of reticulate evolutionary histories across the tree of life. The western rattlesnake species group (C. viridis species complex, C. mitchellii species complex, C. scutulutas, and C. tigris) is an iconic snake lineage that is widespread across western North America. This group is composed of several species complexes with unclear species limits, likely the result of ongoing gene flow among nascent lineages. Here I generate reduced representation genomic data and test for a history of reticulation within this group. I demonstrate that all species have undergone hybridization with at least one other lineage, suggesting introgression is widespread in this group. Topologies differ between phylogenies estimated under the multispecies coalescent and multispecies network coalescent methods, indicating that gene flow has obscured phylogenetic relationships within this group. These past introgression events are predominantly restricted to species that co-occur geographically. However, within species that have a history of introgression, this signature is detected regardless of specimen sampling across geography. Overall, my results suggest the accumulation of reproductive isolating barriers occurs slowly in rattlesnakes which likely leads to the difficulty in delimiting species, furthermore, the results of this study have implications for trait evolution in this group.

The Evolutionary Dynamics of Negative Existentials in Indo-European

Where in earlier work diachronic change is used to explain away exceptions to typologies, linguistic typologists have started to make use of explicit diachronic models as explanations for typological distributions. A topic that lends itself for this approach especially well is that of negation. In this article, we assess the explanatory value of a specific hypothesis, the Negative Existential Cycle (NEC), on the distribution of negative existential strategies (“types”) in 106 Indo-European languages. We use Bayesian phylogenetic comparative methods to infer posterior distributions of transition rates and parameters, thus applying rational methods to construct and evaluate a set of different models under which the attested typological distribution could have evolved. We find that the frequency of diachronic processes that affect negative existentials outside of the NEC cannot be ignored—the unidirectional NEC alone cannot explain the evolution of negative existential strategies in our sample. We show that non-unidirectional evolutionary models, especially those that allow for different and multiple transitions between strategies, provide better fit. In addition, the phylogenetic modeling is impacted by the expected skewed distribution of negative existential strategies in our sample, pointing out the need for densely sampled and family-based typological research.

Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data.

The historical signal in nucleotide sequences becomes eroded over time by substitutions occurring repeatedly at the same sites. This phenomenon, known as substitution saturation, is recognized as one of the primary obstacles to deep-time phylogenetic inference using genome-scale data sets. We present a new test of substitution saturation and demonstrate its performance in simulated and empirical data. For some of the 36 empirical phylogenomic data sets that we examined, we detect substitution saturation in around 50% of loci. We found that saturation tends to be flagged as problematic in loci with highly discordant phylogenetic signals across sites. Within each data set, the loci with smaller numbers of informative sites are more likely to be flagged as containing problematic levels of saturation. The entropy saturation test proposed here is sensitive to high evolutionary rates relative to the evolutionary timeframe, while also being sensitive to several factors known to mislead phylogenetic inference, including short internal branches relative to external branches, short nucleotide sequences, and tree imbalance. Our study demonstrates that excluding loci with substitution saturation can be an effective means of mitigating the negative impact of multiple substitutions on phylogenetic inferences. [Phylogenetic model performance; phylogenomics; substitution model; substitution saturation; test statistics.]

Multiple Sources of Introduction of North American Arabidopsis thaliana from across Eurasia.

Large-scale movement of organisms across their habitable range, or migration, is an important evolutionary process that can shape genetic diversity and influence the adaptive spread of alleles. Although human migrations have been studied in great detail with modern and ancient genomes, recent anthropogenic influence on reducing the biogeographical constraints on the migration of nonnative species has presented opportunities in several study systems to ask the questions about how repeated introductions shape genetic diversity in the introduced range. We present an extensive overview of population structure of North American Arabidopsis thaliana by studying a set of 500 whole-genome sequenced and over 2,800 RAD-seq genotyped individuals in the context of global diversity represented by Afro-Eurasian genomes. We use methods based on haplotype and rare-allele sharing as well as phylogenetic modeling to identify likely sources of introductions of extant N. American A. thaliana from the native range in Africa and Eurasia. We find evidence of admixture among the introduced lineages having increased haplotype diversity and reduced mutational load. We also detect signals of selection in immune-system-related genes that may impart qualitative disease resistance to pathogens of bacterial and oomycete origin. We conclude that multiple introductions to a nonnative range can rapidly enhance the adaptive potential of a colonizing species by increasing haplotypic diversity through admixture. Our results lay the foundation for further investigations into the functional significance of admixture.

Pollinators contribute to the maintenance of flowering plant diversity

Mechanisms that favour rare species are key to the maintenance of diverse communities1-3. One of the most critical tasks for conservation of flowering plant biodiversity is to understand how plant-pollinator interactions contribute to the maintenance of rare species4-7. Here we show that niche partitioning in pollinator use and asymmetric facilitation confer fitness advantage of rarer species in a biodiversity hotspot using phylogenetic structural equation modelling that integrates plant-pollinator and interspecific pollen transfer networks with floral functional traits. Co-flowering species filtered pollinators via floral traits, and rarer species showed greater pollinator specialization leading to higher pollination-mediated male and female fitness than more abundant species. When plants shared pollinator resources, asymmetric facilitation via pollen transport dynamics benefitted the rarer species at the cost of more abundant species, serving as an alternative diversity-promoting mechanism. Our results emphasize the importance of community-wide plant-pollinator interactions that affect reproduction for biodiversity maintenance.

The model-specific Markov embedding problem for symmetric group-based models

We study model embeddability, which is a variation of the famous embedding problem in probability theory, when apart from the requirement that the Markov matrix is the matrix exponential of a rate matrix, we additionally ask that the rate matrix follows the model structure. We provide a characterisation of model embeddable Markov matrices corresponding to symmetric group-based phylogenetic models. In particular, we provide necessary and sufficient conditions in terms of the eigenvalues of symmetric group-based matrices. To showcase our main result on model embeddability, we provide an application to hachimoji models, which are eight-state models for synthetic DNA. Moreover, our main result on model embeddability enables us to compute the volume of the set of model embeddable Markov matrices relative to the volume of other relevant sets of Markov matrices within the model.

Identification of biomolecules for Alzheimer's disease using docking analysis of tau protein

Objective: In-silico methods to find and characterize the ligands against the active site of tau protein which could assist in the therapeutics of Alzheimer's disease. Methods: The aid of various bioinformatic tools such as phylogenetic analysis, homology modeling, and active site prediction led to the molecular docking analysis of the major malefactor for Alzheimer’s disease ‘microtubule- associated tau protein’. A three-dimensional structure of microtubule-related tau protein was created, and the Ramachandran plot was acquired for quality appraisal. Results: Procheck showed 62.95 of residues in the most preferred region with 20% residues in the additional allowed region and 5.7 % in the disallowed region of microtubule-associated tau protein. Screenings of the particles were done dependent on Lipinski's standard of five. Conclusion: Genistein, Hesperidin, and epigallocatechin-3 are the potential ligands in regulating microtubule-related tau protein and Epigallocatechin-3 gallate is the most potent among them and the most elevated negative free vitality of official with the maximum interacting surface territory throughout docking studies.

Taxonomic Uncertainty and the Anomaly Zone: Phylogenomics Disentangle a Rapid Radiation to Resolve Contentious Species (Gila robusta Complex) in the Colorado River.

Species are indisputable units for biodiversity conservation, yet their delimitation is fraught with both conceptual and methodological difficulties. A classic example is the taxonomic controversy surrounding the Gila robusta complex in the lower Colorado River of southwestern North America. Nominal species designations were originally defined according to weakly diagnostic morphological differences, but these conflicted with subsequent genetic analyses. Given this ambiguity, the complex was re-defined as a single polytypic unit, with the proposed “threatened” status under the U.S. Endangered Species Act of two elements being withdrawn. Here we re-evaluated the status of the complex by utilizing dense spatial and genomic sampling (n = 387 and >22 k loci), coupled with SNP-based coalescent and polymorphism-aware phylogenetic models. In doing so, we found that all three species were indeed supported as evolutionarily independent lineages, despite widespread phylogenetic discordance. To juxtapose this discrepancy with previous studies, we first categorized those evolutionary mechanisms driving discordance, then tested (and subsequently rejected) prior hypotheses which argued phylogenetic discord in the complex was driven by the hybrid origin of Gila nigra. The inconsistent patterns of diversity we found within G. robusta were instead associated with rapid Plio-Pleistocene drainage evolution, with subsequent divergence within the “anomaly zone” of tree space producing ambiguities that served to confound prior studies. Our results not only support the resurrection of the three species as distinct entities but also offer an empirical example of how phylogenetic discordance can be categorized within other recalcitrant taxa, particularly when variation is primarily partitioned at the species level.

Aposematism in mammals.

Aposematic coloration is traditionally considered to signal unpalatability or toxicity. In mammals, most research has focused on just one form of defense, namely, noxious anal secretions, and its black-and-white advertisement as exemplified by skunks. The original formulation of aposematism, however, encompassed a broader range of morphological, physiological, and behavioral defenses, and there are many mammal species with black-and-white contrasting patterns that do not have noxious adaptations. Here, using Bayesian phylogenetic models and data from 1726 terrestrial nonvolant mammals we find that two aspects of conspicuous coloration, black-and-white coloration patterns on the head and body, advertise defenses that are morphological (spines, large body size), behavioral (pugnacity), and physiological (anal secretions), as well as being involved with sexual signaling and environmental factors linked to crypsis. Within Carnivora, defensive anal secretions are associated with complex black-and-white head patterns and longitudinal black-and-white body striping; in primates, larger bodied species exhibit irregular patches of black-and-white pelage; and in rodents, pugnacity is linked to sharp countershading and irregular blocks of white and black pelage. We show that black-and-white coloration in mammals is multifunctional, that it serves to warn predators of several defenses other than noxious anal secretions, and that aposematism in mammals is not restricted to carnivores.

Assembly Processes and Co-occurrence Patterns of Abundant and Rare Bacterial Community in the Eastern Indian Ocean.

Microbial communities are composed of many rare species and a few abundant species. Considering the disproportionate importance of rare species for ecosystem functioning, it is important to understand the mechanisms structuring the rare and abundant components of a diverse community in response to environmental changes. Here, we used a 16S ribosomal RNA gene sequencing approach to investigate the bacterial community diversity in the Eastern Indian Ocean (EIO) during the monsoon and intermonsoon. We employed a phylogenetic null model and network analysis to evaluate the assembly processes and co-occurrence pattern of the microbial community. We found that higher bacterial diversity was detected in the intermonsoon with high temperature and low Chlorophyll a concentrations and N/P ratios. The balance between ecological deterministic processes and stochastic processes varied with seasons in the EIO. Meanwhile, conditionally rare taxa (CRT) were more likely modulated by variable selection processes than always rare taxa (ART) and abundant taxa (AT) (CRT > ART > AT). By linking assembly process and species co-occurrence, we demonstrated that the microbial co-occurrence associations tended to be higher when deterministic processes (mainly variable selection) were weaker. This negative trend was observed in rare species rather than abundant species. The linkage could enhance our understanding of the underlying mechanisms underpinning the generation and maintenance of microbial community diversity.

Inferring the factors for origin and diversifications of endemic Himalayan flora using phylogenetic models

Inferring the factors for origin and diversifications of endemic Himalayan flora using phylogenetic models

Haplotype Network Analysis and Phylogenetic Tree Construction of Hepatitis C Virus (HCV) Isolated from Tuban, Indonesia

This study aimed to analyzed the haplotype network and constructed the phylogenetic tree topology of hepatitis C virus (HCV) in Tuban, Indonesia and those from other countries, to determine the visualize genealogical relationship and inference about gene connected. The HCV isolates were collected from blood transfusion center of Tuban, East Java, Indonesia in 2015 and as a comparison, also the sequences of HCV isolates were retrieved from the GenBank®, National Center of Biotechnology Information (NCBI), USA database. To constructed of distribution map was performed through median joining analysis using Haplotype Network v4.6, whereas to constructed and phylogenetic model analyses were constructed based on the NS5B and 5’UTR regions using MEGA X, maximum-likelihood method based on the Tamura-Nei model. In the HCV NS5B region haplotype network showed high haplotype diversity (Hd=1.00) in 22 haplotypes. Based on phylogenetic analysis 3 sample isolates Tuban (BDT-55-p23, BDT-79-p23 and BDT-112-p23) were identified one group and closely related to isolates from Indonesia. However, isolates Tuban also have the same sequence characters as the isolates from Thailand. It was also confirmed in haplotype network that the three isolates are connected to each other. The identification of HCV genotypes circulating in blood donors in the Tuban of East Java confirmed were closely related to HCV isolates from Indonesia and Thailand. Therefore, this result might contribute in a better medical management towards HCV.

Strong support for a heterogeneous speciation decline model in Dinosauria: a response to claims made by Bonsor et al. (2020).

Through phylogenetic modelling, we previously presented strong support for diversification decline in the three major subclades of dinosaurs (Sakamoto et al. 2016 Proc. Natl Acad. Sci. USA 113, 5036–5040. (doi:10.1073/pnas.1521478113)). Recently, our support for this model has been criticized (Bonsor et al. 2020 R. Soc. Open Sci. 7, 201195. (doi:10.1098/rsos.201195)). Here, we highlight that these criticisms seem to largely stem from a misunderstanding of our study: contrary to Bonsor et al.'s claims, our model accounts for heterogeneity in diversification dynamics, was selected based on deviance information criterion (DIC) scores (not parameter significance), and intercepts were estimated to account for uncertainties in the root age of the phylogenetic tree. We also demonstrate that their new analyses are not comparable to our models: they fit simple, Dinosauria-wide models as a direct comparison to our group-wise models, and their additional trees are subclades that are limited in taxonomic coverage and temporal span, i.e. severely affected by incomplete sampling. We further present results of new analyses on larger, better-sampled trees (N = 961) of dinosaurs, showing support for the time-quadratic model. Disagreements in how we interpret modelled diversification dynamics are to be expected, but criticisms should be based on sound logic and understanding of the model under discussion.

Meadow degradation increases spatial turnover rates of the fungal community through both niche selection and dispersal limitation

The alpine meadow ecosystem, as the main ecosystem of the Qinghai-Tibet Plateau, has been heavily degraded over the past several decades due to overgrazing and climate change. Although soil microorganisms play key roles in the stability and succession of grassland ecosystems, their response to grassland degradation has not been investigated at spatial scale. Here, we systematically analyzed the spatial turnover rates of soil prokaryotic and fungal communities in degraded and undegraded meadows through distance-decay relationship (DDR) and species area relationship (SAR), as well as the community assembly mechanisms behind them. Although the composition and structure of both fungal and prokaryotic communities showed significant changes between undegraded and degraded meadows, steeper spatial turnover rates were only observed in fungi (Degraded Alpine Meadow β = 0.0142, Undegraded Alpine Meadow β = 0.0077, P < 0.05). Mantel tests indicated that edaphic variables and vegetation factors showed significant correlations to the β diversity of fungal community only in degraded meadow, suggesting soil and vegetation heterogeneity both contributed to the variation of fungal community in that system. Correspondingly, a novel phylogenetic null model analysis demonstrated that environmental selection was enhanced in the fungal community assembly process during meadow degradation. Interestingly, dispersal limitation was also enhanced for the fungal community in the degraded meadow, and its relative contribution to other assembly process (i.e. selection and drift) showed a significant linear increase with spatial distance, suggesting that dispersal limitation played a greater role as distance increased. Our findings indicated the spatial scaling of the fungal community is altered during meadow degradation by both niche selection and dispersal limitation. This study provides a new perspective for the assessment of soil microbial responses to vegetation changes in alpine areas.

Assessing bite force estimates in extinct mammals and archosaurs using phylogenetic predictions

AbstractBite force is an ecologically important biomechanical performance measure that is informative in inferring the ecology of extinct taxa. However, biomechanical modelling to estimate bite force is associated with some level of uncertainty. Here, I assess the accuracy of bite force estimates in extinct taxa using a Bayesian phylogenetic prediction model. I first fitted a phylogenetic regression model on a training set comprising extant data. The model predicts bite force from body mass and skull width while accounting for differences owing to biting position. The posterior predictive model has a 93% prediction accuracy as evaluated using leave‐one‐out cross‐validation. I then predicted bite force in 37 species of extinct mammals and archosaurs from the posterior distribution of predictive models, generating posterior predictive distributions of null expectations given body mass, skull width and phylogenetic position. Biomechanically estimated bite forces from the literature fall within the posterior predictive distributions for all except four species of extinct taxa and are thus as accurate as predicted from body size and skull width, given the variation inherent in extant taxa and the amount of time available for variance to accrue. Biomechanical modelling remains a valuable means to estimate bite force in extinct taxa and should be reliably informative of functional performances and serve to provide insights into past ecologies.

Diversity patterns and drivers of methanotrophic gene distributions in forest soils across a large latitudinal gradient

AbstractAimMethane oxidation driven by soil aerobic methanotrophs exhibits the largest methane sink capacity in forest ecosystems and plays important roles in the alleviation of global warming. Many studies have revealed the distribution of methanotrophs in forest ecosystems at field scales; however, the biogeographical patterns of methanotrophic communities and related ecological processes and the drivers shaping methanotrophic communities at a large scale remain poorly understood.LocationChina’s forests.Time period2012–2013.Major taxa studiedMethanotrophic communities.MethodsWe evaluated the geographical distributions of soil methanotrophic communities across 26 forests along a 4,000‐km north–south transect in China using a MiSeq high‐throughput sequencing technique. The assembly processes and drivers of the methanotrophic communities were evaluated using the phylogenetic null model approach and structural equation modelling, respectively.ResultsThe results showed that the upland soil cluster α (USCα) and ammonia‐ oxidizing bacteria‐related (AOB‐rel) methanotrophs were the most abundant taxa in forest soils and exhibited contrasting distributions of relative abundance across different climate zones, suggesting that they occupy different environmental niches. The α‐diversity pattern of the soil methanotrophic community followed a hump‐shaped pattern along a large latitudinal gradient. Statistical analyses suggest that aridity and vegetation productivity [here represented with the normalized difference vegetation index (NDVI)] are major drivers of the α‐diversity of the methanotrophic community, whereas soil pH is the key environmental factor shaping the β‐diversity of the methanotrophic community at a large scale. Additionally, the community assembly of the methanotrophs primarily resulted from deterministic processes, among which heterogeneous selection had a greater contribution in shaping the methanotrophic community than homogeneous selection.Main conclusionsOur study provides new insights into the biogeographical distributions, assembly processes and ecological predictors of the methanotrophic community in forest soil at a large scale. These results can be used to improve simulation models for the better prediction of ecosystem functions under predicted global changes.

Evolutionary dynamics of Indo-European alignment patterns

Abstract This paper employs phylogenetic modeling to reconstruct the alignment system of Indo-European. We use a data set of categorical morphosyntactic features, which take states such as ‘nominative-accusative’, ‘active-stative’, or ‘ergative’. We analyze these characters with a standard Bayesian comparative phylogenetic method, inferring transition rates between character states on the basis of a phylogenetic representation of the languages in the data. Using these rates, we then reconstruct the probability of presence of traits at the root and nodes of Indo-European. We find that the most probable alignment system for Proto-Indo-European is a nominative-accusative system, with low probabilities of neutral marking and ergativity in the categories lower in grammatical hierarchies (nouns, past). Using a test of phylogenetic signal, we find that characters pertaining to categories higher in hierarchies show greater phylogenetic stability than categories lower in hierarchies. We examine our results in relation to theories of Proto-Indo-European alignment as well as to general typology.

Evolutionary dynamics of the elevational diversity gradient in passerine birds.

Low-elevation regions harbour the majority of the world's species diversity compared to high-elevation areas. This global gradient suggests that lowland species have had more time to diversify, or that net diversification rates have been higher in the lowlands. However, highlands seem to be cradles of diversity as they contain many young endemics, suggesting that their rates of speciation are exceptionally fast. Here we use a phylogenetic diversification model that accounts for the dispersal of species between different elevations to examine the evolutionary dynamics of the elevational diversity gradient in passerine birds, a group that has radiated globally to occupy almost all elevations and latitudes. We find strong support for a model in which passerines diversify at the same rate in the highlands and the lowlands but in which the per-capita rate of dispersal from high to low elevations is more than twice as fast as that in the reverse direction. This suggests that while there is no consistent trend in diversification across elevations, part of the diversity generated by highland regions migrates into the lowlands, thus setting up the observed gradient in passerine diversity. We find that this process drives tropical regions but for temperate areas, the analysis could be hampered by their lower richness. Despite their lower diversity, highland regions are disproportionally important for maintaining diversity in the adjacent lowlands.