Evolutionary Regimes Research Articles

Signatures of natural selection in tree topology shape of serially sampled viral phylogenies

Tree shape metrics can be computed fast for trees of any size, which makes them promising alternatives to intensive statistical methods and parameter-rich evolutionary models in the era of massive data availability. Previous studies have demonstrated their effectiveness in unveiling important parameters in viral evolutionary dynamics, although the impact of natural selection on the shape of tree topologies has not been thoroughly investigated. We carried out a forward-time and individual-based simulation to investigate whether tree shape metrics of several kinds could predict the selection regime employed to generate the data. To examine the impact of the genetic diversity of the founder viral population, simulations were run under two opposing starting configurations of the genetic diversity of the infecting viral population. We found that four evolutionary regimes, namely, negative, positive, and frequency-dependent selection, as well as neutral evolution, were successfully distinguished by tree topology shape metrics. Two metrics from the Laplacian spectral density profile (principal eigenvalue and peakedness) and the number of cherries were the most informative for indicating selection type. The genetic diversity of the founder population had an impact on differentiating evolutionary scenarios. Tree imbalance, which has been frequently associated with the action of natural selection on intrahost viral diversity, was also characteristic of neutrally evolving serially sampled data. Metrics calculated from empirical analysis of HIV datasets indicated that most tree topologies exhibited shapes closer to the frequency-dependent selection or neutral evolution regimes.

Release from sexual selection leads to rapid genome-wide evolution in Aedes aegypti

The yellow fever mosquito, Aedes aegypti, mates in flight as part of ephemeral aggregations termed swarms. Swarms contain many more males than females, and males are thought to be subject to intense sexual selection.1,2 However, which male traits are involved in mating success and the genetic basis of these traits remains unclear. We used an experimental evolution approach to measure genome-wide responses of Ae. aegypti evolved in the presence and absence of sexual selection. These data revealed for the first time how sexual selection shapes the genome of this important species. We found that populations evolved under sexual selection retained greater genetic similarity to the ancestral population and a higher effective population size than populations evolving without sexual selection. When we compared evolutionary regimes, we found that genes associated with chemosensation responded rapidly to the elimination of sexual selection. Knockdown of one high-confidence candidate gene identified in our analysis significantly decreased male insemination success, further suggesting that genes related to male sensory perception are under sexual selection. Several mosquito control technologies involve the release of males from captive populations into the wild. For these interventions to work, a released male must compete against wild males to successfully inseminate a female. Our results suggest that maintaining the intensity of sexual selection in captive populations used in mass-releases is important for sustaining both male competitive ability and overall genetic similarity to field populations.

Evolution and Spread of Politeness Systems inIndo‐European

AbstractIn this paper, we investigate the phenomenon of pronominal politeness in the Indo‐European languages and demonstrate that the processes of change of pronominal systems related to politeness follow two evolutionary regimes, one inside the ‘Standard Average European’ (SAE) linguistic area and another outside of it. Historical processes of language change differ at different levels of linguistic structure. In general, we presume that lower level, unconscious aspects of language change slowly over phylogenetic time, giving rise to patterns of relationship that can often be described as a family tree. Aspects of language that are consciously manipulated by speakers are expected to vary at a faster rate and to diffuse within areas of contact. Politeness is a social phenomenon, so we expect these systems to be highly susceptible to areal norms of interaction. We show that the similarities of SAE politeness systems can be accounted for with a model of convergence due to parallel evolution in a shared (social‐demographic) environment, rather than by genealogical relatedness or borrowing. By quantifying and testing factors determining rates of structural change, we offer a novel and realistic approach that can explain similarities between distantly related languages sharing the same environment.

Dissipative collapse of cosmic structures in modified gravity

The aim of this work is to analyze the consequences of heat conductivity in evolutionary regimes of axially symmetric cosmic configuration within the context of the Palatini f(R) gravity. The modified gravitational field equations are applied to the proposed configurations. The effects of proposed formalism are observed on kinematical quantities. We study the thermodynamical aspects of the self-gravitating radiating matter configuration coupled with vorticity through transport equation. We also analyze the consequences of effective-inertial-mass-density factor through the coupling of heat conduction and the modified Euler equation. It is discovered that the effective-inertial-mass-density is caused by the interactions between the temperature of the dissipative configuration and the fluid’s four-acceleration. We also explore the time propagation equations for certain kinematical quantities, and examine the influence of Palatini f(R) structure scalars on their evolution. It is concluded that vorticity and the scalars (YI, YII and YKL) play an important role in revealing the significant effects of anisotropy of the source. These constituents govern the shearing motion of our relativistic anisotropic and radiating cosmic configuration.

Evolutionary Genetic Signatures of Selection on Bone-Related Variation within Human and Chimpanzee Populations.

Bone strength and the incidence and severity of skeletal disorders vary significantly among human populations, due in part to underlying genetic differentiation. While clinical models predict that this variation is largely deleterious, natural population variation unrelated to disease can go unnoticed, altering our perception of how natural selection has shaped bone morphologies over deep and recent time periods. Here, we conduct the first comparative population-based genetic analysis of the main bone structural protein gene, collagen type I α 1 (COL1A1), in clinical and 1000 Genomes Project datasets in humans, and in natural populations of chimpanzees. Contrary to predictions from clinical studies, we reveal abundant COL1A1 amino acid variation, predicted to have little association with disease in the natural population. We also find signatures of positive selection associated with intron haplotype structure, linkage disequilibrium, and population differentiation in regions of known gene expression regulation in humans and chimpanzees. These results recall how recent and deep evolutionary regimes can be linked, in that bone morphology differences that developed among vertebrates over 450 million years of evolution are the result of positive selection on subtle type I collagen functional variation segregating within populations over time.

Remarkable intrapopulation venom variability in the monocellate cobra (Naja kaouthia) unveils neglected aspects of India's snakebite problem

Interpopulation venom variation has been widely documented in snakes across large geographical distances. This variability is known to markedly influence the effectiveness of snakebite therapy, as antivenoms manufactured against one population may not be effective against others. In contrast, the extent of intrapopulation venom variability, especially at finer geographical scales, remains largely uninvestigated. Moreover, given the historical focus on the ‘big four’ Indian snakes, our understanding of venom variation in medically important yet neglected snakes, such as the monocellate cobra (Naja kaouthia), remains unclear. To address this shortcoming, we investigated N. kaouthia venoms sampled across a small spatial scale (<50 km) in Eastern India. An interdisciplinary approach employed in this study unveiled considerable intrapopulation differences in the venom proteomic composition, pharmacological and biochemical activities, and toxicity profiles. Documentation of stark differences in venoms at such a finer geographical scale, despite the influence of similar ecological and environmental conditions, is intriguing. Furthermore, evaluation of in vitro and in vivo venom recognition and neutralisation potential of Indian polyvalent ‘big four’ antivenoms and Thai monovalent N. kaouthia antivenom revealed concerning deficiencies. These results highlight the negative impact of phylogenetic divergence and intrapopulation snake venom variation on the effectiveness of conventional antivenom therapy. SignificanceIn contrast to our understanding of snake venom variation across large distances, which is theorised to be shaped by disparities in ecology and environment, intrapopulation variation at finer geographic scales remains scarcely investigated. Assessment of intrapopulation venom variability in Naja kaouthia at a small spatial scale (<50 km) in Eastern India unravelled considerable differences in venom compositions, activities and potencies. While the influence of subtle differences in prey preference and local adaptations cannot be ruled out, these findings, perhaps, also emphasise the role of accelerated molecular evolutionary regimes that rapidly introduce variations in evolutionarily younger lineages, such as advanced snakes. The inability of ‘big four’ Indian antivenoms and Thai N. kaouthia monovalent antivenom in countering these variations highlights the importance of phylogenetic considerations for the development of efficacious snakebite therapy. Thus, we provide valuable insights into the venoms of one of the most medically important yet neglected Indian snakes.

Wonky whales: the evolution of cranial asymmetry in cetaceans

BackgroundUnlike most mammals, toothed whale (Odontoceti) skulls lack symmetry in the nasal and facial (nasofacial) region. This asymmetry is hypothesised to relate to echolocation, which may have evolved in the earliest diverging odontocetes. Early cetaceans (whales, dolphins, and porpoises) such as archaeocetes, namely the protocetids and basilosaurids, have asymmetric rostra, but it is unclear when nasofacial asymmetry evolved during the transition from archaeocetes to modern whales. We used three-dimensional geometric morphometrics and phylogenetic comparative methods to reconstruct the evolution of asymmetry in the skulls of 162 living and extinct cetaceans over 50 million years.ResultsIn archaeocetes, we found asymmetry is prevalent in the rostrum and also in the squamosal, jugal, and orbit, possibly reflecting preservational deformation. Asymmetry in odontocetes is predominant in the nasofacial region. Mysticetes (baleen whales) show symmetry similar to terrestrial artiodactyls such as bovines. The first significant shift in asymmetry occurred in the stem odontocete family Xenorophidae during the Early Oligocene. Further increases in asymmetry occur in the physeteroids in the Late Oligocene, Squalodelphinidae and Platanistidae in the Late Oligocene/Early Miocene, and in the Monodontidae in the Late Miocene/Early Pliocene. Additional episodes of rapid change in odontocete skull asymmetry were found in the Mid-Late Oligocene, a period of rapid evolution and diversification. No high-probability increases or jumps in asymmetry were found in mysticetes or archaeocetes. Unexpectedly, no increases in asymmetry were recovered within the highly asymmetric ziphiids, which may result from the extreme, asymmetric shape of premaxillary crests in these taxa not being captured by landmarks alone.ConclusionsEarly ancestors of living whales had little cranial asymmetry and likely were not able to echolocate. Archaeocetes display high levels of asymmetry in the rostrum, potentially related to directional hearing, which is lost in early neocetes—the taxon including the most recent common ancestor of living cetaceans. Nasofacial asymmetry becomes a significant feature of Odontoceti skulls in the Early Oligocene, reaching its highest levels in extant taxa. Separate evolutionary regimes are reconstructed for odontocetes living in acoustically complex environments, suggesting that these niches impose strong selective pressure on echolocation ability and thus increased cranial asymmetry.

Mutator Gene Model with Three Classes of Evolutionary States

The mutator gene model is one of the fundamental models of modern evolutionary dynamics. Usually, one considers a transition between two evolutionary regimes: the wild-type and mutator type. In thi...

Game-Theoretical Modeling of Interviral Conflicts Mediated by Mini-CRISPR Arrays.

All cellular organisms coevolve with multiple viruses, so that both virus-host and intervirus conflicts are major factors of evolution. Accordingly, hosts evolve multiple, elaborate defense systems and viruses respond by evolving means of antidefense. Although less thoroughly characterized, several dedicated mechanisms of intervirus competition have been described as well. Recently, the genomes of some bacterial and archaeal viruses have been shown to harbor CRISPR mini-arrays that typically contain a single spacer targeting a closely related virus. The involvement of mini-arrays in an intervirus conflict has been experimentally demonstrated for a pair of archaeal viruses. We model the evolution of virus-encoded CRISPR mini-arrays using a game theoretical approach. Analysis of the model reveals multiple equilibria that include mutual targeting, unidirectional targeting, no targeting, cyclic polymorphism, and bistability. The choice between these evolutionary regimes depends on the model parameters including the coinfection frequency, differential productivity of the conflicting viruses, and the fitness cost of mini-arrays. At high coinfection frequencies, the model becomes a version of the Prisoner’s dilemma in which defection, i.e., mutual targeting between the competing viruses, is the winning strategy.

A Multitype Birth-Death Model for Bayesian Inference of Lineage-Specific Birth and Death Rates.

Heterogeneous populations can lead to important differences in birth and death rates across a phylogeny. Taking this heterogeneity into account is necessary to obtain accurate estimates of the underlying population dynamics. We present a new multitype birth–death model (MTBD) that can estimate lineage-specific birth and death rates. This corresponds to estimating lineage-dependent speciation and extinction rates for species phylogenies, and lineage-dependent transmission and recovery rates for pathogen transmission trees. In contrast with previous models, we do not presume to know the trait driving the rate differences, nor do we prohibit the same rates from appearing in different parts of the phylogeny. Using simulated data sets, we show that the MTBD model can reliably infer the presence of multiple evolutionary regimes, their positions in the tree, and the birth and death rates associated with each. We also present a reanalysis of two empirical data sets and compare the results obtained by MTBD and by the existing software BAMM. We compare two implementations of the model, one exact and one approximate (assuming that no rate changes occur in the extinct parts of the tree), and show that the approximation only slightly affects results. The MTBD model is implemented as a package in the Bayesian inference software BEAST 2 and allows joint inference of the phylogeny and the model parameters.[Birth–death; lineage specific rates, multi-type model.]

Computer Simulation of the Evolution of Microbial Population: Overcoming Local Minima When Reaching a Peak on the Fitness Landscape

The study focuses on the mechanisms of crossing the valleys of fitness by a population of haploid microorganisms, whose fitness depends on allelic values at two different loci and is determined by a complex landscape, the shape of which corresponds to the pattern “a mountain in the field surrounded by a trench”; these mechanisms are analyzed using computer modeling. We have studied the influence of various biological factors on the evolutionary perspective of microbial colonies, the reproduction rate of which is controlled by a protein consisting of two subunits encoded at different loci. Molecular genetic (mutation rate, affinity of subunits), population (fitness function landscape and population density), and ecological (concentration of available substrate in the habitat, flow intensity) factors have been considered. Our results demonstrate that the difference in fitness for various allelic combinations, while determining the shape of the fitness landscape, sets the optimal mutation rates to overcome its valleys and opens a window of opportunity for the evolution of the population toward the state of the highest average fitness. Moreover, depending on the fitness landscape type, either gradual or saltational evolutionary regimes are optimal for reaching the peak.

A Bayesian extension of phylogenetic generalized least squares: Incorporating uncertainty in the comparative study of trait relationships and evolutionary rates.

Phylogenetic comparative methods use tree topology, branch lengths, and models of phenotypic change to take into account nonindependence in statistical analysis. However, these methods normally assume that trees and models are known without error. Approaches relying on evolutionary regimes also assume specific distributions of character states across a tree, which often result from ancestral state reconstructions that are subject to uncertainty. Several methods have been proposed to deal with some of these sources of uncertainty, but approaches accounting for all of them are less common. Here, we show how Bayesian statistics facilitates this task while relaxing the homogeneous rate assumption of the well-known phylogenetic generalized least squares (PGLS) framework. This Bayesian formulation allows uncertainty about phylogeny, evolutionary regimes, or other statistical parameters to be taken into account for studies as simple as testing for coevolution in two traits or as complex as testing whether bursts of phenotypic change are associated with evolutionary shifts in intertrait correlations. A mixture of validation approaches indicates that the approach has good inferential properties and predictive performance. We provide suggestions for implementation and show its usefulness by exploring the coevolution of ankle posture and forefoot proportions in Carnivora.

A new, fast method to search for morphological convergence with shape data.

Morphological convergence is an intensely studied macroevolutionary phenomenon. It refers to the morphological resemblance between phylogenetically distant taxa. Currently available methods to explore evolutionary convergence either: rely on the analysis of the phenotypic resemblance between sister clades as compared to their ancestor, fit different evolutionary regimes to different parts of the tree to see whether the same regime explains phenotypic evolution in phylogenetically distant clades, or assess deviations from the congruence between phylogenetic and phenotypic distances. We introduce a new test for morphological convergence working directly with non-ultrametric (i.e. paleontological) as well as ultrametric phylogenies and multivariate data. The method (developed as the function search.conv within the R package RRphylo) tests whether unrelated clades are morphologically more similar to each other than expected by their phylogenetic distance. It additionally permits using known phenotypes as the most recent common ancestors of clades, taking full advantage of fossil information. We assessed the power of search.conv and the incidence of false positives by means of simulations, and then applied it to three well-known and long-discussed cases of (purported) morphological convergence: the evolution of grazing adaptation in the mandible of ungulates with high-crowned molars, the evolution of mandibular shape in sabertooth cats, and the evolution of discrete ecomorphs among anoles of Caribbean islands. The search.conv method was found to be powerful, correctly identifying simulated cases of convergent morphological evolution in 95% of the cases. Type I error rate is as low as 4–6%. We found search.conv is some three orders of magnitude faster than a competing method for testing convergence.

Crossing fitness valleys via double substitutions within codons

BackgroundSingle nucleotide substitutions in protein-coding genes can be divided into synonymous (S), with little fitness effect, and non-synonymous (N) ones that alter amino acids and thus generally have a greater effect. Most of the N substitutions are affected by purifying selection that eliminates them from evolving populations. However, additional mutations of nearby bases potentially could alleviate the deleterious effect of single substitutions, making them subject to positive selection. To elucidate the effects of selection on double substitutions in all codons, it is critical to differentiate selection from mutational biases.ResultsWe addressed the evolutionary regimes of within-codon double substitutions in 37 groups of closely related prokaryotic genomes from diverse phyla by comparing the fractions of double substitutions within codons to those of the equivalent double S substitutions in adjacent codons. Under the assumption that substitutions occur one at a time, all within-codon double substitutions can be represented as “ancestral-intermediate-final” sequences (where “intermediate” refers to the first single substitution and “final” refers to the second substitution) and can be partitioned into four classes: (1) SS, S intermediate–S final; (2) SN, S intermediate–N final; (3) NS, N intermediate–S final; and (4) NN, N intermediate–N final. We found that the selective pressure on the second substitution markedly differs among these classes of double substitutions. Analogous to single S (synonymous) substitutions, SS double substitutions evolve neutrally, whereas analogous to single N (non-synonymous) substitutions, SN double substitutions are subject to purifying selection. In contrast, NS show positive selection on the second step because the original amino acid is recovered. The NN double substitutions are heterogeneous and can be subject to either purifying or positive selection, or evolve neutrally, depending on the amino acid similarity between the final or intermediate and the ancestral states.ConclusionsThe results of the present, comprehensive analysis of the evolutionary landscape of within-codon double substitutions reaffirm the largely conservative regime of protein evolution. However, the second step of a double substitution can be subject to positive selection when the first step is deleterious. Such positive selection can result in frequent crossing of valleys on the fitness landscape.

The Evolutionary Radiation of Hominids: a Phylogenetic Comparative Study

Over the last 150 years the diversity and phylogenetic relationships of the hominoids have been one of the main focuses in biological and anthropological research. Despite this, the study of factors involved in their evolutionary radiation and the origin of the hominin clade, a key subject for the further understanding of human evolution, remained mostly unexplored. Here we quantitatively approach these events using phylogenetic comparative methods and craniofacial morphometric data from extant and fossil hominoid species. Specifically, we explore alternative evolutionary models that allow us to gain new insights into this clade diversification process. Our results show a complex and variable scenario involving different evolutionary regimes through the hominid evolutionary radiation –modeled by Ornstein-Uhlenbeck multi-selective regime and Brownian motion multi-rate scenarios–. These different evolutionary regimes might relate to distinct ecological and cultural factors previously suggested to explain hominid evolution at different evolutionary scales along the last 10 million years.

Automatic generation of evolutionary hypotheses using mixed Gaussian phylogenetic models

Phylogenetic comparative methods are widely used to understand and quantify the evolution of phenotypic traits, based on phylogenetic trees and trait measurements of extant species. Such analyses depend crucially on the underlying model. Gaussian phylogenetic models like Brownian motion and Ornstein-Uhlenbeck processes are the workhorses of modeling continuous-trait evolution. However, these models fit poorly to big trees, because they neglect the heterogeneity of the evolutionary process in different lineages of the tree. Previous works have addressed this issue by introducing shifts in the evolutionary model occurring at inferred points in the tree. However, for computational reasons, in all current implementations, these shifts are "intramodel," meaning that they allow jumps in 1 or 2 model parameters, keeping all other parameters "global" for the entire tree. There is no biological reason to restrict a shift to a single model parameter or, even, to a single type of model. Mixed Gaussian phylogenetic models (MGPMs) incorporate the idea of jointly inferring different types of Gaussian models associated with different parts of the tree. Here, we propose an approximate maximum-likelihood method for fitting MGPMs to comparative data comprising possibly incomplete measurements for several traits from extant and extinct phylogenetically linked species. We applied the method to the largest published tree of mammal species with body- and brain-mass measurements, showing strong statistical support for an MGPM with 12 distinct evolutionary regimes. Based on this result, we state a hypothesis for the evolution of the brain-body-mass allometry over the past 160 million y.

In Situ Measurements of Polymer Micellization Kinetics with Millisecond Temporal Resolution.

Utilizing synchrotron small-angle X-ray scattering (SAXS) integrated with a microfluidic device, micellization kinetics of a diblock co-polymer, poly(ethylene glycol)-b-poly(caprolactone) (PEG-b-PCL) was measured in situ with millisecond temporal and micrometer spatial resolution. The evolutionary regimes of polymer micellization - nucleation, fusion, and insertion were directly observed. The five-inlet microfluidic device provided steady continuous mixing of the polymer solution and the antisolvent. Solvent replacement was mainly dominated by lateral diffusion across the hydrodynamically focused central layer, whose thickness could be precisely designed and manipulated from mass balance of the partitioning streams. Knowing the micellization kinetics of the polymers is essential for design and optimization of self-assembled polymeric nanostructures. The technique of integrating SAXS with microfluidic devices can be translatable to other systems for a breadth of applications.

On and off the rocks: persistence and ecological diversification in a tropical Australian lizard radiation

BackgroundCongruent patterns in the distribution of biodiversity between regions or habitats suggest that key factors such as climatic and topographic variation may predictably shape evolutionary processes. In a number of tropical and arid biomes, genetic analyses are revealing deeper and more localised lineage diversity in rocky ranges than surrounding habitats. Two potential drivers of localised endemism in rocky areas are refugial persistence through climatic change, or ecological diversification and specialisation. Here we examine how patterns of lineage and phenotypic diversity differ across two broad habitat types (rocky ranges and open woodlands) in a small radiation of gecko lizards in the genus Gehyra (the australis group) from the Australian Monsoonal Tropics biome.ResultsUsing a suite of approaches for delineating evolutionarily independent lineages, we find between 26 and 41 putative evolutionary units in the australis group (versus eight species currently recognised). Rocky ranges are home to a greater number of lineages that are also relatively more restricted in distribution, while lineages in open woodland habitats are fewer, more widely distributed, and, in one case, show evidence of range expansion. We infer at least two shifts out of rocky ranges and into surrounding woodlands. Phenotypic divergence between rocky ranges specialist and more generalist taxa is detected, but no convergent evolutionary regimes linked to ecology are inferred.ConclusionsIn climatically unstable biomes such as savannahs, rocky ranges have functioned as zones of persistence, generators of diversity and a source of colonists for surrounding areas. Phenotypic divergence can also be linked to the use of differing habitat types, however, the extent to which ecological specialisation is a primary driver or secondary outcome of localised diversification remains uncertain.

Multiple Components of Phylogenetic Non-stationarity in the Evolution of Brain Size in Fossil Hominins

One outstanding phenotypic character in Homo is its brain evolution. Pagel (Morphology, shape and phylogeny, CRC Press, Boca Raton, 2002) performed a phylogenetic analysis of the evolution of cranial capacity (as a surrogate of brain size) in fossil hominins, finding evidence for gradual evolutionary change with accelerating rate. Since Pagel’s pioneering investigation, the hominin fossil record expanded backward in time, new species were added to our family tree, different phylogenetic hypotheses were advanced, and new phylogenetic comparative methods became available. Therefore, we feel it is timely to repeat and expand upon Pagel’s seminal paper by including such material and applying novel methodologies. We fitted several evolutionary models to the endocranial volume (ECV) for 21 fossil hominins (including Pagel’s original analyses) and estimated phylogenetic signal using different approaches, while accounting for phylogenetic uncertainty. We then applied the phylogenetic signal-representation curve to the data to look for non-stationarity (discontinuities, rate shifts, or presence of different evolutionary patterns in different parts of the phylogeny) in brain size evolution. Our analyses show that, in principle, Pagel’s findings are robust to the addition of new data and phylogenetic uncertainty and confirm both the strong phylogenetic signal in brain size and acceleration of ECV evolutionary rates towards the present. However, non-stationarity was also detected in about 11% of the simulations, with two significant evolutionary discontinuities occurring close to the origin of the H. sapiens lineage (H. sapiens, H. neanderthalensis, H. heidelbergensis and H. antecessor) and along the phyletic line leading to H. floresiensis. This study calls upon further investigation of these important moments in Homo evolution, in order to understand the processes underling each of these shifts in brain size evolutionary regimes.

Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces.

Natural selection is a fundamental force shaping organismal evolution, as it both maintains function and enables adaptation and innovation. Viruses, with their typically short and largely coding genomes, experience strong and diverse selective forces, sometimes acting on timescales that can be directly measured. These selection pressures emerge from an antagonistic interplay between rapidly changing fitness requirements (immune and antiviral responses from hosts, transmission between hosts, or colonization of new host species) and functional imperatives (the ability to infect hosts or host cells and replicate within hosts). Indeed, computational methods to quantify these evolutionary forces using molecular sequence data were initially, dating back to the 1980s, applied to the study of viral pathogens. This preference largely emerged because the strong selective forces are easiest to detect in viruses, and, of course, viruses have clear biomedical relevance. Recent commoditization of affordable high-throughput sequencing has made it possible to generate truly massive genomic data sets, on which powerful and accurate methods can yield a very detailed depiction of when, where, and (sometimes) how viral pathogens respond to various selective forces.Here, we present recent statistical developments and state-of-the-art methods to identify and characterize these selection pressures from protein-coding sequence alignments and phylogenies. Methods described here can reveal critical information about various evolutionary regimes, including whole-gene selection, lineage-specific selection, and site-specific selection acting upon viral genomes, while accounting for confounding biological processes, such as recombination and variation in mutation rates.