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203 results for “Divergence times”
Data from: Bayesian estimation of species divergence times using correlated quantitative characters
Discrete morphological data have been widely used to study species evolution, but the use of quantitative (or continuous) morphological characters is less common. Here, we implement a Bayesian method to estimate species divergence times using quantitative characters. Quantitative character evolution is modelled using Brownian diffusion with character correlation and character variation within populations. Through simulations, we demonstrate that ignoring the population variation (or population "noise") and the correlation among characters leads to biased estimates of divergence times and rate, especially if the correlation and population noise are high. We apply our new method to the analysis of quantitative characters (cranium landmarks) and molecular data from carnivoran mammals. Our results show that time estimates are affected by whether the correlations and population noise are accounted for or ignored in the analysis. The estimates are also affected by the type of data analysed, with analyses of morphological characters only, molecular data only, or a combination of both; showing noticeable differences among the time estimates. Rate variation of morphological characters among the carnivoran species appears to be very high, with Bayesian model selection indicating that the independent-rates model fits the morphological data better than the autocorrelated-rates model. We suggest that using morphological continuous characters, together with molecular data, can bring a new perspective to the study of species evolution. Our new model is implemented in the MCMCtree computer program for Bayesian inference of divergence times.
Data from: Phylogenetic informativeness reconciles ray-finned fish molecular divergence times
Discordance among individual molecular age estimates, or between molecular age estimates and the fossil record, is observed in many clades across the Tree of Life. This discordance is attributed to a variety of variables including calibration age uncertainty, calibration placement, nucleotide substitution rate heterogeneity, or the specified molecular clock model. However, the impact of changes in phylogenetic informativeness of individual genes over time on phylogenetic inferences is rarely analyzed. Using nuclear and mitochondrial sequence data for ray-finned fishes (Actinopterygii) as an example, we extend the utility of phylogenetic informativeness profiles to predict the time intervals when nucleotide substitution saturation results in discordance among molecular ages estimated. Results: We demonstrate that even with identical calibration regimes and molecular clock methods, mitochondrial based molecular age estimates are systematically older than those estimated from nuclear sequences. This discordance is most severe for highly nested nodes corresponding to more recent (i.e., Jurassic-Recent) divergences. By removing data deemed saturated, we reconcile the competing age estimates and highlight that the older mtDNA based ages were driven by nucleotide saturation. Conclusions: Homoplasious site patterns in a DNA sequence alignment can systematically bias molecular divergence time estimates. Our study demonstrates that PI profiles can provide a non-arbitrary criterion for data exclusion to mitigate the influence of homoplasy on time calibrated branch length estimates. Analyses of actinopterygian molecular clocks demonstrate that scrutiny of the time scale on which sequence data is informative is a fundamental, but generally overlooked, step in molecular divergence time estimation.
Data from: Hemocyanin gene family evolution in spiders (Araneae), with implications for phylogenetic relationships and divergence times in the infraorder Mygalomorphae
Hemocyanins are multimeric copper-containing hemolymph proteins involved in oxygen binding and transport in all major arthropod lineages. Most arachnids have seven primary subunits (encoded by paralogous genes a–g), which combine to form a 24-mer (4 × 6) quaternary structure. Within some spider lineages, however, hemocyanin evolution has been a dynamic process with extensive paralog duplication and loss. We have obtained hemocyanin gene sequences from numerous representatives of the spider infraorders Mygalomorphae and Araneomorphae in order to infer the evolution of the hemocyanin gene family and estimate spider relationships using these conserved loci. Our hemocyanin gene tree is largely consistent with the previous hypotheses of paralog relationships based on immunological studies, but reveals some discrepancies in which paralog types have been lost or duplicated in specific spider lineages. Analyses of concatenated hemocyanin sequences resolved deep nodes in the spider phylogeny and recovered a number of clades that are supported by other molecular studies, particularly for mygalomorph taxa. The concatenated data set is also used to estimate dates of higher-level spider divergences and suggests that the diversification of extant mygalomorphs preceded that of extant araneomorphs. Spiders are diverse in behavior and respiratory morphology, and our results are beneficial for the comparative analyses of spider respiration. Lastly, the conserved hemocyanin sequences allow for the inference of spider relationships and ancient divergence dates.
Data from: Using phylogenomic data to explore the effects of relaxed clocks and calibration strategies on divergence time estimation: primates as a test case
Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the K-Pg boundary and the timing of diversification of the main crown groups remain controversial. Here we analysed a dataset of 372 taxa (367 Primates and 5 outgroups, 3.4 million aligned base pairs) that includes nine primate genomes. We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates. We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (auto-correlated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient age estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the auto-correlated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred. We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K-Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene.
Data from: Fossils, molecules, divergence times, and the origin of Lissamphibians
A review of the paleontological literature shows that the early dates of appearance of Lissamphibia recently inferred from molecular data do not favor an origin of extant amphibians from temnospondyls, contrary to recent claims. A supertree is assembled using new Mesquite modules that allow extinct taxa to be incorporated into a time-calibrated phylogeny with a user-defined geological time scale. The supertree incorporates 223 extinct species of lissamphibians and has a highly significant stratigraphic fit. Some divergences can even be dated with sufficient precision to serve as calibration points in molecular divergence date analyses. Fourteen combinations of minimal branch length settings and 10 random resolutions for each polytomy give much more recent minimal origination times of lissamphibian taxa than recent studies based on a phylogenetic analyses of molecular sequences. Attempts to replicate recent molecular date estimates show that these estimates depend strongly on the choice of calibration points, on the dating method, and on the chosen model of evolution; for instance, the estimate for the date of the origin of Lissamphibia can lie between 351 and 266 Mya. This range of values is generally compatible with our time-calibrated supertree and indicates that there is no unbridgeable gap between dates obtained using the fossil record and those using molecular evidence, contrary to previous suggestions.
Data from: Morphology, fossils, divergence timing, and the phylogenetic relationships of Gavialis
Although morphological data have historically favored a basal position for the Indian gharial (Gavialis gangeticus) within Crocodylia and a Mesozoic divergence between Gavialis and all other crocodylians, several recent molecular data sets have argued for a sister-group relationship between Gavialis and the Indonesian false gharial (Tomistoma schlegelii) and a divergence between them no earlier than the Late Tertiary. Fossils were added to a matrix of 164 discrete morphological characters and subjected to parsimony analysis. When morphology was analyzed alone, Gavialis was the sister taxon of all other extant crocodylians whether or not fossil ingroup taxa were included, and a sister-group relationship between Gavialis and Tomistoma was significantly less parsimonious. In combination with published sequence and restriction site fragment data, Gavialis was the sister taxon of all other living crocodylians, but the position of Tomistoma depended on the inclusion of fossil ingroup taxa; with or without fossils, preferred morphological and molecular topologies were not significantly different. Fossils closer to Gavialis than to Tomistoma can be recognized in the Late Cretaceous, and fossil relatives of Tomistoma are known from the basal Eocene, strongly indicating a divergence long before the Late Tertiary. Comparison of minimum divergence time from the fossil record with different measures of molecular distance indicates evolutionary rate heterogeneity within Crocodylia. Fossils strongly contradict a post-Oligocene divergence between Gavialis and any other living crocodylian, but the phylogenetic placement of Gavialis is best viewed as unresolved.
Data from: Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales)
Although temporal calibration is widely recognized as critical for obtaining accurate divergence-time estimates using molecular dating methods, few studies have evaluated the variation resulting from different calibration strategies. Depending on the information available, researchers have often used primary calibrations from the fossil record or secondary calibrations from previous molecular dating studies. In analyses of flowering plants, primary calibration data can be obtained from macro- and mesofossils (e.g., leaves, flowers, and fruits) or microfossils (e.g., pollen). Fossil data can vary substantially in accuracy and precision, presenting a difficult choice when selecting appropriate calibrations. Here, we test the impact of eight plausible calibration scenarios for Nothofagus (Nothofagaceae, Fagales), a plant genus with a particularly rich and well-studied fossil record. To do so, we reviewed the phylogenetic placement and geochronology of 38 fossil taxa of Nothofagus and other Fagales, and we identified minimum age constraints for up to 18 nodes of the phylogeny of Fagales. Molecular dating analyses were conducted for each scenario using maximum likelihood (RAxML + r8s) and Bayesian (BEAST) approaches on sequence data from six regions of the chloroplast and nuclear genomes. Using either ingroup or outgroup constraints, or both, led to similar age estimates, except near strongly influential calibration nodes. Using 'early but risky' fossil constraints in addition to 'safe but late' constraints, or using assumptions of vicariance instead of fossil constraints, led to older age estimates. In contrast, using secondary calibration points yielded drastically younger age estimates. This empirical study highlights the critical influence of calibration on molecular dating analyses. Even in a best-case situation, with many thoroughly vetted fossils available, substantial uncertainties can remain in the estimates of divergence times. For example, our estimates for the crown-group age of Nothofagus varied from 13 to 113 Ma across our full range of calibration scenarios. We suggest that increased background research should be made at all stages of the calibration process to reduce errors wherever possible, from verifying the geochronological data on the fossils to critical re-assessment of their phylogenetic position.
Estimating uncertainty in divergence times among three-spined stickleback clades using the multispecies coalescent
<p>Incomplete lineage sorting (ILS) can lead to biased divergence time estimates. To explore if and how ILS has influenced the results of a recent study of worldwide phylogeny of three-spined sticklebacks (Gasterosteus aculeatus), we estimated divergence times among major clades by applying both a concatenation approach and the multispecies coalescent (MSC) model to single-nucleotide polymorphisms. To further test the influence of different calibration strategies, we applied different calibrations to the root and to younger nodes in addition to the ones used in the original study. Both the updated calibrations and the application of the MSC model influenced divergence time estimates, sometimes significantly. The new divergence time estimates were more ancient than in the previous study for older nodes, whereas the estimates of younger nodes were not strongly affected by the re-analyses. However, given the applied MSC method employs a simple substitution model and cannot account for changes in population size, we suggest that different analytical approaches and calibration strategies should be used in order to explore uncertainty in divergence time estimates. This study provides a valuable reference timeline for the ages of worldwide three-spined stickleback populations and emphasizes the need to embrace, rather than obscure, uncertainties around divergence time estimates.</p>
Data from: Divergent selection on, but no genetic conflict over, female and male timing and rate of reproduction in a human population
The sexes often have different phenotypic optima for important life-history traits, and because of a largely shared genome this can lead to a conflict over trait expression. In mammals, the obligate costs of reproduction are higher for females, making reproductive timing and rate especially liable to conflict between the sexes. While studies from wild vertebrates support such sexual conflict, it remains unexplored in humans. We used a pedigreed human population from preindustrial Finland to estimate sexual conflict over age at first and last reproduction, reproductive lifespan and reproductive rate. We found that the phenotypic selection gradients differed between the sexes. We next established significant heritabilities in both sexes for all traits. All traits, except reproductive rate, showed strongly positive intersexual genetic correlations and were strongly genetically correlated with fitness in both sexes. Moreover, the genetic correlations with fitness were almost identical in men and women. For reproductive rate, the intersexual correlation and the correlation with fitness were weaker but again similar between the sexes. Thus, in this population, an apparent sexual conflict at the phenotypic level did not reflect an underlying genetic conflict over the studied reproductive traits. These findings emphasize the need for incorporating genetic perspectives into studies of human life-history evolution.
FIGURE 2. Penaeini ultrametric tree. Below a in Molecular phylogeny and divergence time estimates of Penaeid Shrimp Lineages (Decapoda: Penaeidae)
FIGURE 2. Penaeini ultrametric tree. Below a geological time-scale is shown.
Reconstruction of reticulate evolution and divergence timing based on RNA-seq: Hippophae as a case
<p>Phylotranscriptomic analysis has successfully been used to reconstruct phylogenies of higher taxa. However, depicting the patterns of phylogenies in more details and, especially, estimating time of introgression for lower taxa remain challenging. Here, we selected Hippophae (Elaeagnaceae), a small genus restricted to the Qinghai-Tibet Plateau (QTP) and adjacent areas, as an example to optimize approaches to investigate reticulate evolution in lower taxa with RNA-seq. Plastid genes and low copy nuclear genes were extracted from RNA-seq data to reconstruct a reliable species tree of Hippophae and estimate the time of species divergence, respectively. Results show that the phylogeny of five Hippophae species has been consistently solved except for H. salicifolia and a potential hybrid species. The divergence time of 5 species ranged from 17.56 Ma to 6.04 Ma, the era of the Himalayas uplift. The inconsistence between gene trees was integrated with the implicit network analysis approaches, such as investigating statistical difference of anomalous gene trees and asymmetry of average most recent common ancestor (MRCA) ages, and explicit network analysis approaches, such as PhyloNet and SNaQ. At least two separate introgression cases were involved in the history of Hippophae: one took place between two basial clades of this genus, in which an early member or common ancestor of H. rhamnoides and H. thibetana lineages experienced introgression with an early member or common ancestor of H. neurocarpa and H. gyantsensis; the other was between H. gyantsensis and H. neurocarpa. Using a MCMC fitting model, we estimated the secondary divergence time after the first introgression, finding two secondary divergence times: one was about 8.79 (7.05-10.64) Ma and between H. rhamnoides and the MRCA of H. neurocarpa and H. gyantsensis, and the other was near 7.76 (5.89-9.58) Ma and between H. tibetana and the MRCA of H. neurocarpa and H. gyantsensis. Furthermore, introgressed gene candidates, including some potential adaptive genes, were found, indicating that even the introgression in small genus is important and functional for species differentiation. Based on the above results and previous studies, the reticulate evolution of Hippophae was highlighted, providing a potential guidance in using RNA-seq data for reconstructing the complex evolution history of lower taxa.</p>
Data from: Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia
Were molecular data available for extinct taxa, questions regarding the origins of many groups could be settled in short order. As this is not the case, various strategies have been proposed to combine paleontological and neontological datasets. The use of fossil dates as node age calibrations for divergence time estimation from molecular phylogenies is commonplace. In addition, simulations suggest that the addition of morphological data from extinct taxa may improve phylogenetic estimation when combined with molecular data for extant species, and a few studies have combined morphological and molecular data to estimate combined-evidence phylogenies containing both fossil and extant taxa. However, to date, few if any studies have attempted to infer divergence time estimates using phylogenies containing both extinct and living taxa, sampled for both molecular and morphological data. Here, I infer both the phylogeny and time of origin for Lissamphibia using Bayesian methods, based on a dataset containing morphological data for extinct taxa, molecular data for a number of extant species, and molecular and morphological data for a subset of extant taxa. The results suggest that Lissamphibia is monophyletic, nested within Lepospondyli, and originated in the late Carboniferous at the earliest. This research illustrates potential pitfalls for the use of fossils as post-hoc age constraints on internal nodes, and highlights the importance of explicit phylogenetic analysis of extinct taxa. These results suggest that the application of fossils as minima or maxima on molecular phylogenies should be supplemented or supplanted by combined-evidence analyses whenever possible.
Figure 4 from: Del Latte L, Bortolin F, Rota-Stabelli O, Fusco G, Bonato L (2015) Molecular-based estimate of species number, phylogenetic relationships and divergence times for the genus Stenotaenia (Chilopoda, Geophilomorpha) in the Italian region. In: Tuf IH, Tajovský K (Eds) Proceedings of the 16th International Congress of Myriapodology, Olomouc, Czech Republic. ZooKeys 510: 31-47. https://doi.org/10.3897/zookeys.510.8808
Figure 4 - Dated phylogeny. Estimates of divergence time, calculated using 28S sequences and two priors (age of the root and substitution rate) in the package BEAST v1.7.2 (see text). 95% High Posterior Density intervals are represented by coloured bars for the most robust nodes, emphasized by a circle. Greek letters refer to the species tentatively recognised (see Fig. 1). The tree has the same topology of the concatenated ML tree of Fig. 3, but for the position of Tuoba sydneyensis and the relationships within the group formed by species β, ε, γ and the specimen from Iran. The specimen from Volpago (species δ) is absent because its 28S sequence was not obtained. Time scale is different in the two intervals 0–100 and 100–200 Ma.
Figure 3 from: Del Latte L, Bortolin F, Rota-Stabelli O, Fusco G, Bonato L (2015) Molecular-based estimate of species number, phylogenetic relationships and divergence times for the genus Stenotaenia (Chilopoda, Geophilomorpha) in the Italian region. In: Tuf IH, Tajovský K (Eds) Proceedings of the 16th International Congress of Myriapodology, Olomouc, Czech Republic. ZooKeys 510: 31-47. https://doi.org/10.3897/zookeys.510.8808
Figure 3 - Maximum likelihood phylogeny. ML tree obtained from concatenated COI and 28S sequences, by the GTR+I+G model, and manually rooted. The following support values are indicated at the nodes (only for those present in the topology obtained from the concatenated sequences): ML bootstrap for the analysis of concatenated genes (upper left); Bayesian posterior probabilities (upper right, in italics); ML bootstrap for the analysis of COI sequences (lower left); ML bootstrap for the analysis of 28S sequences (lower right). Bootstrap values < 50% and posterior probabilities < 0.50 are not shown. Circles indicate ingroup nodes that are highly supported in the tree based on concatenated sequences. Terminal node groupings indicated by Greek letters refer to the species tentatively recognized (see text and Fig. 1). The specimen from Volpago (species δ) is absent because its 28S sequence was not obtained.
Figure 1 from: Del Latte L, Bortolin F, Rota-Stabelli O, Fusco G, Bonato L (2015) Molecular-based estimate of species number, phylogenetic relationships and divergence times for the genus Stenotaenia (Chilopoda, Geophilomorpha) in the Italian region. In: Tuf IH, Tajovský K (Eds) Proceedings of the 16th International Congress of Myriapodology, Olomouc, Czech Republic. ZooKeys 510: 31-47. https://doi.org/10.3897/zookeys.510.8808
Figure 1 - Sampling localities of Stenotaenia in the Italian region. Greek letters refer to the species tentatively recognized after the analyses (see text).
Figure 1 in Mitogenomes resolve the phylogeography and divergence times within the endemic New Zealand Callaeidae (Aves: Passerida)
Figure 1. Callaeidae, or New Zealand wattlebirds, showing key phenotypic differences between North and South Island forms of Philesturnus and Callaeas. Differences in plumage between North and South Island Philesturnus are exaggerated for clarity.
Figure 6 in Reassessing the phylogeny and divergence times of sloths (Mammalia: Pilosa: Folivora), exploring alternative morphological partitioning and dating models
Figure 6. Estimated rate multipliers for homoplasy-based partitions in each model.
Data and code for "Terrestrial water cycle acceleration-deceleration: Non-binary and space-time divergent"
<p>This dataset provides all data compiled and generated for the manuscript entitled "Terrestrial water cycle acceleration-deceleration: Non-binary and space-time divergent" (manuscript under consideration). This includes the boundaries for 3614 hydrological catchments, the curated data used for analysis and modelling, the developed machine learning model, shapley values and area of applicability results, and data for global extrapolation</p> <p>It also contains the code in a Quarto file ('Code.qmd') and a markdown file ('Code.html') which shows how to access and use the data, and generic sample codes used to generate these results.</p> <p> </p> <p>Code - R session info:</p> <p>R version 4.2.1 (2022-06-23 ucrt)</p> <p>Platform: x86_64-w64-mingw32/x64 (64-bit)</p> <p>Running under: Windows 10 x64 (build 22621)</p> <p>Matrix products: default locale: [1] LC_COLLATE=Portuguese_Brazil.utf8 LC_CTYPE=Portuguese_Brazil.utf8 [3] LC_MONETARY=Portuguese_Brazil.utf8 LC_NUMERIC=C [5] LC_TIME=Portuguese_Brazil.utf8</p> <p>attached base packages: [1] stats [2] graphics [3] grDevices [4] utils [5] datasets [6] methods [7] base</p> <p>other attached packages: [1] bundle_0.0.0.9200 [2] stacks_1.0.0 [3] bonsai_0.1.0 [4] rules_1.0.0 [5] finetune_0.2.0 [6] yardstick_1.0.0 [7] workflowsets_1.0.0 [8] workflows_1.0.0 [9] tune_1.0.0 [10] tibble_3.1.7 [11] rsample_1.0.0 [12] recipes_1.0.1 [13] purrr_0.3.4 [14] parsnip_1.0.0 [15] modeldata_1.0.0 [16] infer_1.0.2 [17] dials_1.0.0 [18] scales_1.2.0 [19] broom_1.0.0 [20] tidymodels_1.0.0 [21] ggplot2_3.3.6 [22] rnaturalearth_0.1.0 [23] sf_1.0-8 [24] terra_1.6-3 [25] lubridate_1.8.0 [26] stringr_1.4.0 [27] tidyr_1.2.0 [28] dplyr_1.0.9 [29] pacman_0.5.1</p>
Supplementary material 1 from: Gavrilov VM, Golubeva TB, Bushuev AV (2023) Metabolic rate, sleep duration, and body temperature in evolution of mammals and birds: the influence of geological time of principal groups divergence. ZooKeys 1148: 1-27. https://doi.org/10.3897/zookeys.1148.93458
Mammalian Basal metabolic rate (BMR) dafrom Genoud et al. (2017)
Supplementary material 2 from: Gavrilov VM, Golubeva TB, Bushuev AV (2023) Metabolic rate, sleep duration, and body temperature in evolution of mammals and birds: the influence of geological time of principal groups divergence. ZooKeys 1148: 1-27. https://doi.org/10.3897/zookeys.1148.93458
Aves BMR
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