Data from: Comparing cal3 and other a posteriori time-scaling approaches in a case study with the pterocephaliid trilobites
Contributors: Bapst, David W., Hopkins, Melanie J.
... Reconstructing the tree of life involves more than identifying relationships among lineages; it also entails accurately estimating when lineages diverged. Paleontologists typically scale cladograms to time a posteriori by direct reference to first appearances of taxa in the stratigraphic record. Some approaches use probabilistic models of branching, extinction, and sampling processes to date samples of trees, such as the recently developed cal3 method, which stochastically draws divergence dates given a set of rates for those processes. However, these models require estimates of the rates of those processes, which may be hard to obtain, particularly for sampling. Here, we contrast the use of cal3 and other a posteriori time-scaling approaches by examining a previous study that documented a decelerating rate of morphological evolution in pterocephaliid trilobites. Although aspects of the data set make estimation of branching, extinction, and sampling rates difficult, we use a multifaceted approach to calculate and evaluate the rate estimates needed for applying cal3. In agreement with previous simulation studies, we find that the choice of phylogenetic dating method impacts downstream macroevolutionary conclusions. We also find contradictory evolutionary inferences between analyses on ancestor–descendant contrasts (based on ancestor trait reconstruction methods) and maximum-likelihood parameter estimates. Ancestral taxon inference in cal3 corroborates previously hypothesized ancestor–descendant sequences, but cal3 suggests greater support for budding cladogenesis than anagenesis. This case study demonstrates the potential and wide applicability of the cal3 method and the benefits afforded by choosing cal3 over simpler a posteriori time-scaling approaches.
Contributors: Matzke, Nicholas J., Wright, April
... Tip-dating methods are becoming popular alternatives to traditional node calibration approaches for building time-scaled phylogenetic trees, but questions remain about their application to empirical datasets. We compared the performance of the most popular methods against a dated tree of fossil Canidae derived from previously published monographs. Using a canid morphology dataset, we performed tip-dating using BEAST v. 2.1.3 and MrBayes v. 3.2.5. We find that for key nodes (Canis, approx. 3.2 Ma, Caninae approx. 11.7 Ma) a non-mechanistic model using a uniform tree prior produces estimates that are unrealistically old (27.5, 38.9 Ma). Mechanistic models (incorporating lineage birth, death and sampling rates) estimate ages that are closely in line with prior research. We provide a discussion of these two families of models (mechanistic versus non-mechanistic) and their applicability to fossil datasets.
Data from: Using spatial capture–recapture to elucidate population processes and space-use in herpetological studies
Contributors: Muñoz, David J., Miller, David A. W., Sutherland, Chris, Campbell Grant, Evan H.
... The cryptic behavior and ecology of herpetofauna make estimating the impacts of environmental change on demography difficult; yet, the ability to measure demographic relationships is essential for elucidating mechanisms leading to the population declines reported for herpetofauna worldwide. Recently developed spatial capture–recapture (SCR) methods are well suited to standard herpetofauna monitoring approaches. Individually identifying animals and their locations allows accurate estimates of population densities and survival. Spatial capture–recapture methods also allow estimation of parameters describing space-use and movement, which generally are expensive or difficult to obtain using other methods. In this paper, we discuss the basic components of SCR models, the available software for conducting analyses, and the experimental designs based on common herpetological survey methods. We then apply SCR models to Red-backed Salamander (Plethodon cinereus), to determine differences in density, survival, dispersal, and space-use between adult male and female salamanders. By highlighting the capabilities of SCR, and its advantages compared to traditional methods, we hope to give herpetologists the resource they need to apply SCR in their own systems.
Data from: Genome-wide differentiation in closely related populations: the roles of selection and geographic isolation
Contributors: Safran, Rebecca J., Scordato, Elizabeth S. C., Wilkins, Matthew R., Hubbard, Joanna K., Jenkins, Brittany R., Albrecht, Tomas, Flaxman, Samuel M., Karaardic, Hakan, Vortman, Yoni, Lotem, Arnon
... Population divergence in geographic isolation is due to a combination of factors. Natural and sexual selection may be important in shaping patterns of population differentiation, a pattern referred to as ‘isolation by adaptation’ (IBA). IBA can be complementary to the well-known pattern of ‘isolation by distance’ (IBD), in which the divergence of closely related populations (via any evolutionary process) is associated with geographic isolation. The barn swallow Hirundo rustica complex comprises six closely related subspecies, where divergent sexual selection is associated with phenotypic differentiation among allopatric populations. To investigate the relative contributions of selection and geographic distance to genome-wide differentiation, we compared genotypic and phenotypic variation from 350 barn swallows sampled across eight populations (28 pairwise comparisons) from four different subspecies. We report a draft whole-genome sequence for H. rustica, to which we aligned a set of 9493 single nucleotide polymorphisms (SNPs). Using statistical approaches to control for spatial autocorrelation of phenotypic variables and geographic distance, we find that divergence in traits related to migratory behaviour and sexual signalling, as well as geographic distance, together explain over 70% of genome-wide divergence among populations. Controlling for IBD, we find 42% of genomewide divergence is attributable to IBA through pairwise differences in traits related to migratory behaviour and sexual signalling alone. By (i) combining these results with prior studies of how selection shapes morphological differentiation and (ii) accounting for spatial autocorrelation, we infer that morphological adaptation plays a large role in shaping population-level differentiation in this group of closely related populations.
Data from: The impact of phylogenetic dating method on interpreting trait evolution: a case study of Cretaceous–Palaeogene eutherian body-size evolution
Contributors: Halliday, Thomas J.D., Goswami, Anjali
... The fossil record of the earliest Cenozoic contains the first large-bodied placental mammals. Several evolutionary models have been invoked to explain the transition from small to large body sizes, but methods for determining evolutionary mode of trait change depend on input from tree topology and divergence dates. Different dating methods may therefore affect inference of evolutionary model. Here, we fit models of body mass evolution onto dated phylogenies of Cretaceous and Palaeogene mammals, comparing the effect of dating method on interpretation of evolutionary model. Among traditional palaeontological dating approaches, an Ornstein–Uhlenbeck model with high alpha parameters is recovered as best-fitting when minimum-age dating is used, while branch-sharing methods are highly sensitive to topology. Release or release–radiate models are preferred when Bayesian fossilized birth–death method is used, but when using stochastic cal3 dating of trees, a model of increased evolutionary rate without a release in constraint at the Cretaceous–Palaeogene boundary has highest support. These results demonstrate unambiguously that choice of dating method is critical for interpretation of continuous trait evolution, and that care must therefore be taken to consider these effects in macroevolutionary studies.
Data from: Genome-wide SNP data suggests complex ancestry of sympatric North Pacific killer whale ecotypes
Contributors: Foote, Andrew D., Morin, Phillip A.
... Three ecotypes of killer whale occur in partial sympatry in the North Pacific. Individuals assortatively mate within the same ecotype, resulting in correlated ecological and genetic differentiation. A key question is whether this pattern of evolutionary divergence is an example of incipient sympatric speciation from a single panmictic ancestral population, or whether sympatry could have resulted from multiple colonisations of the North Pacific and secondary contact between ecotypes. Here, we infer multilocus coalescent trees from >1000 nuclear single-nucleotide polymorphisms (SNPs) and find evidence of incomplete lineage sorting so that the genealogies of SNPs do not all conform to a single topology. To disentangle whether uncertainty in the phylogenetic inference of the relationships among ecotypes could also result from ancestral admixture events we reconstructed the relationship among the ecotypes as an admixture graph and estimated f4-statistics using TreeMix. The results were consistent with episodes of admixture between two of the North Pacific ecotypes and the two outgroups (populations from the Southern Ocean and the North Atlantic). Gene flow may have occurred via unsampled ‘ghost’ populations rather than directly between the populations sampled here. Our results indicate that because of ancestral admixture events and incomplete lineage sorting, a single bifurcating tree does not fully describe the relationship among these populations. The data are therefore most consistent with the genomic variation among North Pacific killer whale ecotypes resulting from multiple colonisation events, and secondary contact may have facilitated evolutionary divergence. Thus, the present-day populations of North Pacific killer whale ecotypes have a complex ancestry, confounding the tree-based inference of ancestral geography.
Data from: Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria)
Contributors: Bapst, David W., Wright, April M., Matzke, Nick J., Lloyd, Graeme T.
... Dated phylogenies of fossil taxa allow palaeobiologists to estimate the timing of major divergences and placement of extinct lineages, and to test macroevolutionary hypotheses. Recently developed Bayesian ‘tip-dating’ methods simultaneously infer and date the branching relationships among fossil taxa, and infer putative ancestral relationships. Using a previously published dataset for extinct theropod dinosaurs, we contrast the dated relationships inferred by several tip-dating approaches and evaluate potential downstream effects on phylogenetic comparative methods. We also compare tip-dating analyses to maximum-parsimony trees time-scaled via alternative a posteriori approaches including via the probabilistic cal3 method. Among tip-dating analyses, we find opposing but strongly supported relationships, despite similarity in inferred ancestors. Overall, tip-dating methods infer divergence dates often millions (or tens of millions) of years older than the earliest stratigraphic appearance of that clade. Model-comparison analyses of the pattern of body-size evolution found that the support for evolutionary mode can vary across and between tree samples from cal3 and tip-dating approaches. These differences suggest that model and software choice in dating analyses can have a substantial impact on the dated phylogenies obtained and broader evolutionary inferences.
Data from: Para-allopatry in hybridizing fire-bellied toads (Bombina bombina and B. variegata): inference from transcriptome-wide coalescence analyses
Contributors: Nürnberger, Beate, Lohse, Konrad, Fijarczyk, Anna, Szymura, Jacek M., Blaxter, Mark L.
... Ancient origins, profound ecological divergence, and extensive hybridization make the fire-bellied toads Bombina bombina and B. variegata (Anura: Bombinatoridae) an intriguing test case of ecological speciation. Previous modeling has proposed that the narrow Bombina hybrid zones represent strong barriers to neutral introgression. We test this prediction by inferring the rate of gene exchange between pure populations on either side of the intensively studied Kraków transect. We developed a method to extract high confidence sets of orthologous genes from de novo transcriptome assemblies, fitted a range of divergence models to these data and assessed their relative support with analytic likelihood calculations. There was clear evidence for postdivergence gene flow, but, as expected, no perceptible signal of recent introgression via the nearby hybrid zone. The analysis of two additional Bombina taxa (B. v. scabra and B. orientalis) validated our parameter estimates against a larger set of prior expectations. Despite substantial cumulative introgression over millions of years, adaptive divergence of the hybridizing taxa is essentially unaffected by their lack of reproductive isolation. Extended distribution ranges also buffer them against small-scale environmental perturbations that have been shown to reverse the speciation process in other, more recent ecotypes.
Data from: Continental-scale biogeographic variation: provinces versus gradients in the Upper Ordovician of Laurentia
Contributors: Jenkins, Chelsea E., Holland, Steven M.
... Although provinces are widely used to delimit large-scale variations in biotic composition, it is unknown to what extent such variations simply reflect large-scale gradients, much as has been shown at smaller scales for communities. We examine here whether four previously described Middle and Late Ordovician provinces on Laurentia are best described as distinct provinces or as biotic gradients through a combination of the Paleobiology Database and new field data. Both data sets indicate considerable overlap in faunal composition, with spatial patterns in Jaccard similarity, quantified Jaccard similarity, and nonmetric multidimensional scaling ordination structure that correspond to variations in substrate type, specifically from carbonate-dominated strata in western Laurentia to mixed carbonate–siliciclastic strata in the midcontinent to siliciclastic-dominated rocks in easternmost Laurentia. Because sampling was limited to shallow-subtidal settings, this gradient cannot be attributed to variations in water depth. Likewise, geographic distance accounts for only a quarter of the variation in faunal composition. This cross-continent faunal gradient increases in strength into the early Late Ordovician, and appears to represent increased siliciclastic influx into eastern Laurentia during the Taconic orogeny. These results raise the question of whether biogeographic provinces may be in general better interpreted and analyzed as biotic gradients rather than as discrete entities.
Data from: Food availability and predation risk, rather than intrinsic attributes are the main factors shaping the reproductive decisions of a long-lived predator
Contributors: Hoy, Sarah R, Millon, Alexandre, Petty, Steve J, Whitfield, D Philip, Lambin, Xavier
... Deciphering the causes of variation in reproductive success is a fundamental issue in ecology, as the number of offspring produced is an important driver of individual fitness and population dynamics. Little is known however, about how different factors interact to drive variation in reproduction, such as whether an individual's response to extrinsic conditions (e.g. food availability or predation) varies according to its intrinsic attributes (e.g. age, previous allocation of resources towards reproduction). We used 29 years of reproductive data from marked female tawny owls and natural variation in food availability (field vole) and predator abundance (northern goshawk) to quantify the extent to which extrinsic and intrinsic factors interact to influence owl reproductive traits (breeding propensity, clutch size and nest abandonment). Extrinsic and intrinsic factors appeared to interact to affect breeding propensity (which accounted for 83% of the variation in owl reproductive success). Breeding propensity increased with vole density, although increasing goshawk abundance reduced the strength of this relationship. Owls became slightly more likely to breed as they aged, although this was only apparent for individuals who had fledged chicks the year before. Owls laid larger clutches when food was more abundant. When owls were breeding in territories less exposed to goshawk predation, 99.5% of all breeding attempts reached the fledging stage. In contrast, the probability of breeding attempts reaching the fledging stage in territories more exposed to goshawk predation depended on the amount of resources an owl had already allocated towards reproduction (averaging 87.7% for owls with clutches of 1-2 eggs compared to 97.5% for owls with clutches of 4-6 eggs). Overall, our results suggested that changes in extrinsic conditions (predominantly food availability, but also predator abundance) had the greatest influence on owl reproduction. In response to deteriorating extrinsic conditions (fewer voles and more goshawks) owls appeared to breed more frequently, but allocated fewer resources per breeding attempt. However, intrinsic attributes also appeared to have a relatively small influence on how an individual responded to variation in extrinsic conditions, which indicates that reproductive decisions were shaped by a complex series of extrinsic and intrinsic trade-offs.