Ancient and modern genomes unravel the evolutionary history of the rhinoceros family.

Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.

Complexity of avian evolution revealed by family-level genomes.

Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions1-3. Here we address these issues by analysing the genomes of 363 bird species4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.

The Limits of the Constant-rate Birth-Death Prior for Phylogenetic Tree Topology Inference.

Birth-death models are stochastic processes describing speciation and extinction through time and across taxa and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under the constant-rate birth-death (crBD) model tend to differ from empirical trees, for example, with respect to the amount of phylogenetic imbalance. However, our understanding of how trees differ between the crBD model and the signal in empirical data remains incomplete. In this Point of View, we aim to expose the degree to which the crBD model differs from empirically inferred phylogenies and test the limits of the model in practice. Using a wide range of topology indices to compare crBD expectations against a comprehensive dataset of 1189 empirically estimated trees, we confirm that crBD model trees frequently differ topologically compared with empirical trees. To place this in the context of standard practice in the field, we conducted a meta-analysis for a subset of the empirical studies. When comparing studies that used Bayesian methods and crBD priors with those that used other non-crBD priors and non-Bayesian methods (i.e., maximum likelihood methods), we do not find any significant differences in tree topology inferences. To scrutinize this finding for the case of highly imbalanced trees, we selected the 100 trees with the greatest imbalance from our dataset, simulated sequence data for these tree topologies under various evolutionary rates, and re-inferred the trees under maximum likelihood and using the crBD model in a Bayesian setting. We find that when the substitution rate is low, the crBD prior results in overly balanced trees, but the tendency is negligible when substitution rates are sufficiently high. Overall, our findings demonstrate the general robustness of crBD priors across a broad range of phylogenetic inference scenarios but also highlight that empirically observed phylogenetic imbalance is highly improbable under the crBD model, leading to systematic bias in data sets with limited information content.

Phylo2Vec: a vector representation for binary trees.

Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art methods rely on carefully designed heuristics for tree search, using different data structures for easy manipulation (e.g., classes in object-oriented programming languages) and readable representation of trees (e.g., Newick-format strings). Here, we present Phylo2Vec, a parsimonious encoding for phylogenetic trees that serves as a unified approach for both manipulating and representing phylogenetic trees. Phylo2Vec maps any binary tree with n leaves to a unique integer vector of length n - 1. The advantages of Phylo2Vec are fourfold: i) fast tree sampling, (ii) compressed tree representation compared to a Newick string, iii) quick and unambiguous verification if two binary trees are identical topologically, and iv) systematic ability to traverse tree space in very large or small jumps. As a proof of concept, we use Phylo2Vec for maximum likelihood inference on five real-world datasets and show that a simple hill-climbing-based optimisation scheme can efficiently traverse the vastness of tree space from a random to an optimal tree.

Holmium:yttrium-aluminium-garnet laser with MOSES technology is more efficient than thulium fibre laser in supine mini-percutaneous nephrolithotomy.

OBJECTIVES: To address the paucity of literature comparing outcomes achieved with utilisation of the high-power holmium:yttrium-aluminium-garnet (Ho:YAG) laser with MOSES technology vs those achieved with the thulium fibre laser (TFL) in mini-percutaneous nephrolithotomy (PCNL). METHODS: A retrospective review was performed of patients undergoing supine mini-PCNL between August 2021 and May 2023. Exclusion criteria were urinary diversion, simultaneous utilisation of >1 laser platform, use of any other form of fragmentation, and ureteric stones. The Ho:YAG platform (Lumenis Pulse P120H™ with MOSES technology, 120W; Boston Scientific®) and the TFL (Soltive SuperPulsed Thulium Fibre [SPTF], 60W; Olympus®) were compared. Data on stone-free rate (SFR) were determined by computed tomography performed on the first postoperative day and presented as absence of stone fragments, no fragments larger than 2 mm, or no fragments larger than 4 mm. RESULTS: A total of 100 patients met the inclusion criteria, 51 mini-PCNLs with the Ho:YAG laser and 49 with the SPTF laser. No significant differences in demographics or stone characteristics were detected between the two groups. The Ho:YAG laser utilised less energy and time, resulting in higher ablation efficiency (P < 0.05) and less total operating time (P < 0.05). Overall, there was no difference in SFR in any category between the Ho:YAG group and the SPTF group (no fragments: relative risk [RR] 0.81, 95% confidence interval [CI] 0.59-1.12, P = 0.21; fragments <2 mm: RR 0.86, 95% CI 0.67-1.10, P = 0.23; fragments <4 mm: RR 0.96, 95% CI 0.80-1.15, P = 0.67). CONCLUSIONS: Although we observed an equivalent postoperative SFR, this study supports a shorter operating time and greater intra-operative laser efficiency with the Ho:YAG laser over the SPTF laser in mini-PCNL.

Blue Turns to Gray: Paleogenomic Insights into the Evolutionary History and Extinction of the Blue Antelope (Hippotragus leucophaeus).

The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (Hippotragus equinus) or sable (Hippotragus niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are generally unfavorable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4× mean coverage from a historical specimen (∼200 years old) and one at 2.1× mean coverage from a fossil specimen dating to 9,800-9,300 cal years BP, making it currently the oldest paleogenome from Africa. Phylogenomic analyses show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelope, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene-Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely the decisive factor in the blue antelope's extinction.

A genomic assessment of the marine-speciation paradox within the toothed whale superfamily Delphinoidea.

The impact of post-divergence gene flow in speciation has been documented across a range of taxa in recent years, and may have been especially widespread in highly mobile, wide-ranging marine species, such as cetaceans. Here, we studied individual genomes from nine species across the three families of the toothed whale superfamily Delphinoidea (Delphinidae, Phocoenidae and Monodontidae). To investigate the role of post-divergence gene flow in the speciation process, we used a multifaceted approach, including (i) phylogenomics, (ii) the distribution of shared derived alleles and (iii) demographic inference. We found the divergence of lineages within Delphinoidea did not follow a process of pure bifurcation, but was much more complex. Sliding-window phylogenomics reveal a high prevalence of discordant topologies within the superfamily, with further analyses indicating these discordances arose due to both incomplete lineage sorting and gene flow. D-statistics and f-branch analyses supported gene flow between members of Delphinoidea, with the vast majority of gene flow occurring as ancient interfamilial events. Demographic analyses provided evidence that introgressive gene flow has likely ceased between all species pairs tested, despite reports of contemporary interspecific hybrids. Our study provides the first steps towards resolving the large complexity of speciation within Delphinoidea; we reveal the prevalence of ancient interfamilial gene flow events prior to the diversification of each family, and suggest that contemporary hybridisation events may be disadvantageous, as hybrid individuals do not appear to contribute to the parental species' gene pools.

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.].

Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference.

Phylogenetic analyses of genomic data provide a powerful means of reconstructing the evolutionary relationships among organisms, yet such analyses are often hindered by conflicting phylogenetic signals among loci. Identifying the signals that are most influential to species-tree estimation can help to inform the choice of data for phylogenomic analysis. We investigated this in an analysis of 30 phylogenomic data sets. For each data set, we examined the association between several branch-length characteristics of gene trees and the distance between these gene trees and the corresponding species trees. We found that the distance of each gene tree to the species tree inferred from the full data set was positively associated with variation in root-to-tip distances and negatively associated with mean branch support. However, no such associations were found for gene-tree length, a measure of the overall substitution rate at each locus. We further explored the usefulness of the best-performing branch-based characteristics for selecting loci for phylogenomic analyses. We found that loci that yield gene trees with high variation in root-to-tip distances have a disproportionately distant signal of tree topology compared with the complete data sets. These results suggest that rate variation across lineages should be taken into consideration when exploring and even selecting loci for phylogenomic analysis.[Branch support; data filtering; nucleotide substitution model; phylogenomics; substitution rate; summary coalescent methods.].

On the rocks: can urologists identify stone composition based on endoscopic images alone? A worldwide survey of urologists.

PURPOSE: As part of the management of nephrolithiasis, determination of chemical composition of stones is important. Our objective in this study is to assess urologists' accuracy in making visual, intraoperative determinations of stone composition. MATERIALS AND METHODS: We conducted a REDCap survey asking urologists to predict stone composition based on intraoperative images of 10 different pure-composition kidney stones of 7 different types: calcium oxalate monohydrate (COM), calcium oxalate dihydrate (COD), calcium phosphate (CP) apatite, CP brushite, uric acid (UA), struvite (ST) and cystine (CY). To evaluate experience, we examined specific endourologic training, years of experience, and number of ureteroscopy (URS) cases/week. A self-assessment of ability to identify stone composition was also required. RESULTS: With a response rate of 26% (366 completed surveys out of 1,370 deliveries), the overall accuracy of our cohort was 44%. COM, ST, and COD obtained the most successful identification rates (65.9%, 55.7%, and 52.0%, respectively). The most frequent misidentified stones were CP apatite (10.7%) and CY (14.2%). Predictors of increased overall accuracy included self-perceived ability to determine composition and number of ureteroscopies per week, while years of experience did not show a positive correlation. CONCLUSIONS: Although endoscopic stone recognition can be an important tool for surgeons, it is not reliable enough to be utilized as a single method for stone identification, suggesting that urologists need to refine their ability to successfully recognize specific stone compositions intraoperatively.

Ecological Specialization and Evolutionary Reticulation in Extant Hyaenidae.

During the Miocene, Hyaenidae was a highly diverse family of Carnivora that has since been severely reduced to four species: the bone-cracking spotted, striped, and brown hyenas, and the specialized insectivorous aardwolf. Previous studies investigated the evolutionary histories of the spotted and brown hyenas, but little is known about the remaining two species. Moreover, the genomic underpinnings of scavenging and insectivory, defining traits of the extant species, remain elusive. Here, we generated an aardwolf genome and analyzed it together with the remaining three species to reveal their evolutionary relationships, genomic underpinnings of their scavenging and insectivorous lifestyles, and their respective genetic diversities and demographic histories. High levels of phylogenetic discordance suggest gene flow between the aardwolf lineage and the ancestral brown/striped hyena lineage. Genes related to immunity and digestion in the bone-cracking hyenas and craniofacial development in the aardwolf showed the strongest signals of selection, suggesting putative key adaptations to carrion and termite feeding, respectively. A family-wide expansion in olfactory receptor genes suggests that an acute sense of smell was a key early adaptation. Finally, we report very low levels of genetic diversity within the brown and striped hyenas despite no signs of inbreeding, putatively linked to their similarly slow decline in effective population size over the last ∼2 million years. High levels of genetic diversity and more stable population sizes through time are seen in the spotted hyena and aardwolf. Taken together, our findings highlight how ecological specialization can impact the evolutionary history, demographics, and adaptive genetic changes of an evolutionary lineage.

Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae.

Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes and searching for species-specific structural variants. Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For example, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observed species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined (single nucleotide polymorphisms, gene family expansions, structural variants) contributed substantially to the identification of candidate loci. This argues strongly for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance.

Bird lineages colonizing urban habitats have diversified at high rates across deep time.

Aim: Urbanization exposes species to novel ecological conditions. Some species thrive in urban areas, whereas many others are excluded from these human-made environments. Previous analyses suggest that the ability to cope with rapid environmental change is associated with long-term patterns of diversification, but whether the suite of traits associated with the ability to colonize urban environments is linked to this process remains poorly understood. Location: World. Time period: Current. Major taxa studied: Passerine birds. Methods: We applied macroevolutionary models to a large dataset of passerine birds to compare the evolutionary history of urban-tolerant species with that of urban-avoidant species. Specifically, we examined models of state-dependent speciation and extinction to assess the macroevolution of urban tolerance as a binary trait, in addition to models of quantitative trait-dependent diversification based on relative urban abundance. We also ran simulation-based model assessments to explore potential sources of bias. Results: We provide evidence that historically, species with traits promoting urban colonization have undergone faster diversification than urban-avoidant species, indicating that urbanization favours clades with a historical tendency towards rapid speciation or reduced extinction. In addition, we find that past transitions towards states that currently impede urban colonization by passerines have been more frequent than in the opposite direction. Furthermore, we find a portion of urban-avoidant passerines to be recent and to undergo fast diversification. All highly supported models give this result consistently. Main conclusions: Urbanization is mainly associated with the loss of lineages that are inherently more vulnerable to extinction over deep time, whereas cities tend to be colonized by less vulnerable lineages, for which urbanization might be neutral or positive in terms of longer-term diversification. Urban avoidance is associated with high rates of recent diversification for some clades occurring in regions with relatively intact natural ecosystems and low current levels of urbanization.

Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations.

Phylogenetic methods can use the sampling times of molecular sequence data to calibrate the molecular clock, enabling the estimation of evolutionary rates and timescales for rapidly evolving pathogens and data sets containing ancient DNA samples. A key aspect of such calibrations is whether a sufficient amount of molecular evolution has occurred over the sampling time window, that is, whether the data can be treated as having come from a measurably evolving population. Here, we investigate the performance of a fully Bayesian evaluation of temporal signal (BETS) in sequence data. The method involves comparing the fit to the data of two models: a model in which the data are accompanied by the actual (heterochronous) sampling times, and a model in which the samples are constrained to be contemporaneous (isochronous). We conducted simulations under a wide range of conditions to demonstrate that BETS accurately classifies data sets according to whether they contain temporal signal or not, even when there is substantial among-lineage rate variation. We explore the behavior of this classification in analyses of five empirical data sets: modern samples of A/H1N1 influenza virus, the bacterium Bordetella pertussis, coronaviruses from mammalian hosts, ancient DNA from Hepatitis B virus, and mitochondrial genomes of dog species. Our results indicate that BETS is an effective alternative to other tests of temporal signal. In particular, this method has the key advantage of allowing a coherent assessment of the entire model, including the molecular clock and tree prior which are essential aspects of Bayesian phylodynamic analyses.

Linking Branch Lengths across Sets of Loci Provides the Highest Statistical Support for Phylogenetic Inference.

Evolution leaves heterogeneous patterns of nucleotide variation across the genome, with different loci subject to varying degrees of mutation, selection, and drift. In phylogenetics, the potential impacts of partitioning sequence data for the assignment of substitution models are well appreciated. In contrast, the treatment of branch lengths has received far less attention. In this study, we examined the effects of linking and unlinking branch-length parameters across loci or subsets of loci. By analyzing a range of empirical data sets, we find consistent support for a model in which branch lengths are proportionate between subsets of loci: gene trees share the same pattern of branch lengths, but form subsets that vary in their overall tree lengths. These models had substantially better statistical support than models that assume identical branch lengths across gene trees, or those in which genes form subsets with distinct branch-length patterns. We show using simulations and empirical data that the complexity of the branch-length model with the highest support depends on the length of the sequence alignment and on the numbers of taxa and loci in the data set. Our findings suggest that models in which branch lengths are proportionate between subsets have the highest statistical support under the conditions that are most commonly seen in practice. The results of our study have implications for model selection, computational efficiency, and experimental design in phylogenomics.

A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth-Death Process.

Bayesian molecular dating is widely used to study evolutionary timescales. This procedure usually involves phylogenetic analysis of nucleotide sequence data, with fossil-based calibrations applied as age constraints on internal nodes of the tree. An alternative approach is tip-dating, which explicitly includes fossil data in the analysis. This can be done, for example, through the joint analysis of molecular data from present-day taxa and morphological data from both extant and fossil taxa. In the context of tip-dating, an important development has been the fossilized birth-death process, which allows non-contemporaneous tips and sampled ancestors while providing a model of lineage diversification for the prior on the tree topology and internal node times. However, tip-dating with fossils faces a number of considerable challenges, especially, those associated with fossil sampling and evolutionary models for morphological characters. We conducted a simulation study to evaluate the performance of tip-dating using the fossilized birth-death model. We simulated fossil occurrences and the evolution of nucleotide sequences and morphological characters under a wide range of conditions. Our analyses of these data show that the number and the maximum age of fossil occurrences have a greater influence than the degree of among-lineage rate variation or the number of morphological characters on estimates of node times and the tree topology. Tip-dating with the fossilized birth-death model generally performs well in recovering the relationships among extant taxa but has difficulties in correctly placing fossil taxa in the tree and identifying the number of sampled ancestors. The method yields accurate estimates of the ages of the root and crown group, although the precision of these estimates varies with the probability of fossil occurrence. The exclusion of morphological characters results in a slight overestimation of node times, whereas the exclusion of nucleotide sequences has a negative impact on inference of the tree topology. Our results provide an overview of the performance of tip-dating using the fossilized birth-death model, which will inform further development of the method and its application to key questions in evolutionary biology.

Accounting for Uncertainty in the Evolutionary Timescale of Green Plants Through Clock-Partitioning and Fossil Calibration Strategies.

Establishing an accurate evolutionary timescale for green plants (Viridiplantae) is essential to understanding their interaction and coevolution with the Earth's climate and the many organisms that rely on green plants. Despite being the focus of numerous studies, the timing of the origin of green plants and the divergence of major clades within this group remain highly controversial. Here, we infer the evolutionary timescale of green plants by analyzing 81 protein-coding genes from 99 chloroplast genomes, using a core set of 21 fossil calibrations. We test the sensitivity of our divergence-time estimates to various components of Bayesian molecular dating, including the tree topology, clock models, clock-partitioning schemes, rate priors, and fossil calibrations. We find that the choice of clock model affects date estimation and that the independent-rates model provides a better fit to the data than the autocorrelated-rates model. Varying the rate prior and tree topology had little impact on age estimates, with far greater differences observed among calibration choices and clock-partitioning schemes. Our analyses yield date estimates ranging from the Paleoproterozoic to Mesoproterozoic for crown-group green plants, and from the Ediacaran to Middle Ordovician for crown-group land plants. We present divergence-time estimates of the major groups of green plants that take into account various sources of uncertainty. Our proposed timeline lays the foundation for further investigations into how green plants shaped the global climate and ecosystems, and how embryophytes became dominant in terrestrial environments.

Stone size on endoscopic view as a predictor of successful stone retrieval during flexible ureteroscopy: an in vitro analysis.

PURPOSE: Basketing plays an important role during flexible ureteroscopy, but it can be time-consuming, especially when fragments are too large to pass through the ureteral access sheath. We aim to present the optimal on-screen, endoscopic stone size that predicts successful basketing through various access sheaths. METHODS: A tipless basket, individually extended to 5 mm from multiple ureteroscopes: (Flex-Xc, Karl Storz; Flex-X2s, Karl Storz; LithoVue, Boston Scientific; or URF-P6R, Olympus) and via differently sized access sheaths (10-12 Fr through 13-15 Fr), was used in retrieval attempts of various artificial stone sizes (2 mm through 5 mm). A relative endoscopic stone size was recorded as the stone's maximum diameter on endoscopic view compared to the total image diameter. RESULTS: Basketing of stones up to 2.5 mm, yielding relative endoscopic stone sizes of 0.38 (Flex-Xc), 0.30 (Flex-X2s), 0.32 (LithoVue), and 0.34 (URF-P6R), was successful using all access sheaths. Only the 12-14 Fr and greater sheaths allowed for successful basketing of 3 mm stones. Larger stones did not successfully pass through any of the access sheaths. CONCLUSION: Successful stone retrieval can be predicted by estimating the stone's size on screen, which is influenced by the type of flexible ureteroscope and access sheath. In our testing, stones of approximately one-third of the screen size passed successfully in all cases.

Phylodynamic Model Adequacy Using Posterior Predictive Simulations.

Rapidly evolving pathogens, such as viruses and bacteria, accumulate genetic change at a similar timescale over which their epidemiological processes occur, such that, it is possible to make inferences about their infectious spread using phylogenetic time-trees. For this purpose it is necessary to choose a phylodynamic model. However, the resulting inferences are contingent on whether the model adequately describes key features of the data. Model adequacy methods allow formal rejection of a model if it cannot generate the main features of the data. We present TreeModelAdequacy, a package for the popular BEAST2 software that allows assessing the adequacy of phylodynamic models. We illustrate its utility by analyzing phylogenetic trees from two viral outbreaks of Ebola and H1N1 influenza. The main features of the Ebola data were adequately described by the coalescent exponential-growth model, whereas the H1N1 influenza data were best described by the birth-death susceptible-infected-recovered model.

Sexual selection, body mass and molecular evolution interact to predict diversification in birds.

Sexual selection is a powerful agent of evolution, driving microevolutionary changes in the genome and macroevolutionary rates of lineage diversification. The mechanisms by which sexual selection might influence macroevolution remain poorly understood. For example, sexual selection might drive positive selection for key adaptations that facilitate diversification. Furthermore, sexual selection might be a general driver of molecular evolutionary rate. We lay out some of the potential mechanisms that create a link between sexual selection and diversification, based on causal effects on other life-history traits such as body mass and the rate of molecular evolution. Birds are ideally suited for testing the importance of these relationships because of their diverse reproductive systems and the multiple evolutionary radiations that have produced their astounding modern diversity. We show that sexual selection (measured as the degree of polygyny) interacts with the rate of molecular evolution and with body mass to predict species richness at the genus level. A high degree of polygyny and rapid molecular evolution are positively associated with the net rate of diversification, with the two factors being especially important for explaining diversification in large-bodied taxa. Our findings further suggest that mutation rates underpin some of the macroevolutionary effects of sexual selection. We synthesize the existing theory on sexual selection as a force for diversity and propose avenues for exploring this association using genome data.