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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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

ABSTRACT: Molecular dating analyses allow evolutionary timescales to be estimated from genetic data, offering an unprecedented capacity for investigating the evolutionary past of all species. These methods require us to make assumptions about the relationship between genetic change and evolutionary time, often referred to as a ‘molecular clock’. Although initially regarded with scepticism, molecular dating has now been adopted in many areas of biology. This broad uptake has been due partly to the development of Bayesian methods that allow complex aspects of molecular evolution, such as variation in rates of change across lineages, to be taken into account. But in order to do this, Bayesian dating methods rely on a range of assumptions about the evolutionary process, which vary in their degree of biological realism and empirical support. These assumptions can have substantial impacts on the estimates produced by molecular dating analyses. The aim of this review is to open the ‘black box’ of Bayesian molecular dating and have a look at the machinery inside. We explain the components of these dating methods, the important decisions that researchers must make in their analyses, and the factors that need to be considered when interpreting results. We illustrate the effects that the choices of different models and priors can have on the outcome of the analysis, and suggest ways to explore these impacts. We describe some major research directions that may improve the reliability of Bayesian dating. The goal of our review is to help researchers to make informed choices when using Bayesian phylogenetic methods to estimate evolutionary rates and timescales. [ABSTRACT FROM AUTHOR]

Aim Recent research suggests that the latitudinal diversity gradient ( LDG) in birds is unlikely to result from faster diversification in the tropics. This puts the focus on other mechanisms, such as dispersal, as the primary drivers for the LDG. We aim to distinguish two prominent models, tropical conservatism ( TCH) and out of the tropics ( OTM), which make distinct predictions about dispersal across latitudes and the phylogenetic clustering of assemblages in temperate regions. Location Global. Methods We used geographic and phylogenetic data for more than 9000 bird species to reconstruct the ancestral latitudinal zone for each node in each of 100 bird phylogenetic estimates. We used methods that consider discrete latitudinal zones, as well as those that consider latitudinal position as a continuous variable. We then estimated the frequency of ancestor-descendant dispersal within and across latitudinal zones. We also quantified phylogenetic clustering in latitudinal zones separately for bird assemblages within the Old World and the New World. Results Latitudinal distributions are relatively conserved: 60-96% of nodes had the same inferred latitude as their immediate ancestral node. We find that dispersal events out of the tropics were less frequent (4-5%) than dispersal events into the tropics (15-21%), the opposite of what would be expected under the OTM. Nodes with inferred temperate distributions are generally younger than the Eocene-Oligocene Climate Transition, as expected under the TCH. Phylogenetic clustering shows no regular patterns of association with latitude, and is likely to be largely driven by radiations within a few large forested biomes. Main conclusions Our results provide support for the expectations of the TCH, but are less consistent with those of the OTM. Both the deeper origins of tropical clades and the comparatively recent but infrequent dispersal events into temperate regions appear to play a role in generating the strong disparity in tropical and temperate species richness in birds. [ABSTRACT FROM AUTHOR]

Phylogenetic estimation of evolutionary timescales has become routine in biology, forming the basis of a wide range of evolutionary and ecological studies. However, there are various sources of bias that can affect these estimates. We investigated whether tree imbalance, a property that is commonly observed in phylogenetic trees, can lead to reduced accuracy or precision of phylogenetic timescale estimates. We analysed simulated data sets with calibrations at internal nodes and at the tips, taking into consideration different calibration schemes and levels of tree imbalance. We also investigated the effect of tree imbalance on two empirical data sets: mitogenomes from primates and serial samples of the African swine fever virus. In analyses calibrated using dated, heterochronous tips, we found that tree imbalance had a detrimental impact on precision and produced a bias in which the overall timescale was underestimated. A pronounced effect was observed in analyses with shallow calibrations. The greatest decreases in accuracy usually occurred in the age estimates for medium and deep nodes of the tree. In contrast, analyses calibrated at internal nodes did not display a reduction in estimation accuracy or precision due to tree imbalance. Our results suggest that molecular-clock analyses can be improved by increasing taxon sampling, with the specific aims of including deeper calibrations, breaking up long branches and reducing tree imbalance. [ABSTRACT FROM AUTHOR]

Evolutionary timescales can be estimated from genetic data using phylogenetic methods based on the molecular clock. To account for molecular rate variation among lineages, a number of relaxed-clock models have been developed. Some of these models assume that rates vary among lineages in an autocorrelated manner, so that closely related species share similar rates. In contrast, uncorrelated relaxed clocks allow all of the branch-specific rates to be drawn from a single distribution, without assuming any correlation between rates along neighbouring branches. There is uncertainty about which of these two classes of relaxed-clock models are more appropriate for biological data. We present an R package, NELSI, that allows the evolution of DNA sequences to be simulated according to a range of clock models. Using data generated by this package, we assessed the ability of two Bayesian phylogenetic methods to distinguish among different relaxed-clock models and to quantify rate variation among lineages. The results of our analyses show that rate autocorrelation is typically difficult to detect, even when there is complete taxon sampling. This provides a potential explanation for past failures to detect rate autocorrelation in a range of data sets. [ABSTRACT FROM AUTHOR]