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45 results for “divergence dates”
Data from: Influence of gene flow on divergence dating – implications for speciation history of Takydromus grass lizards
Dating the time of divergence and understanding speciation processes are central to the study of the evolutionary history of organisms but are notoriously difficult. The difficulty is largely rooted in variations in the ancestral population size or in the genealogy variation across loci. To depict the speciation processes and divergence histories of three monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear loci and combined with one mitochondrial locus published in GenBank. They were analyzed by a multispecies coalescent approach within a Bayesian framework. Divergence dating based on the gene tree approach showed high variation among loci, and the divergence was estimated at an earlier date than when derived by the species tree approach. To test whether variations in the ancestral population size accounted for the majority of this variation, we conducted computer inferences using isolation-with-migration (IM) and approximate Bayesian computation (ABC) frameworks. The results revealed that gene flow during the early stage of speciation was strongly favored over the isolation model, and the initiation of the speciation process was far earlier than the dates estimated by gene- and species-based divergence dating. Due to their limited dispersal ability, it is suggested that geographic isolation may have played a major role in the divergence of these Takydromus species. Nevertheless, the current study reveals a more complex situation and demonstrates that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating. By using multilocus data and incorporating Bayesian coalescence approaches, we provide a more biologically realistic framework for delineating the divergence history of Takydromus.
Phylogenetic relationships and divergence dating of Mantodea using mitochondrial phylogenomics
<p>Mantodea is a predatory insect group, its members occupying a diverse array of widely distributed habitats. Praying mantis species utilize hunting strategies including remarkable mimicry and unique camouflage for hiding from natural enemies while catching their prey. The emergence of a "cyclopean ear" in mantises is thought to be a morphological innovation of the group, and an "arms race" with echolocating bats is one of the hypotheses put forward to account for the emergence of the mantis ear from a coevolutionary perspective. However, this hypothesis has not been rigorously tested because of a lack of robust higher‐level phylogeny and a detailed chronogram of Mantodea. Previous phylogenetic studies found an incongruence between traditional classification and molecular phylogenetics due to the convergent evolution of various ecomorphic strategies of the lineage. Here, we performed a comprehensive phylogenetic analysis of Mantodea based on data from 61 mitogenomes. Our analyses showed that the monophyly of Acanthopidae, Haaniidae, Nanomantidae, Miomantidae and Mantidea was supported. The newly updated Gonypetidae were paraphyletic, whereas Eremiaphilidae, Deroplatyidae and Toxoderidae were polyphyletic. Our molecular dating analyses inferred that Spinomantodea originated at ca. 149 Ma (Late Jurassic), whereas the origin of hearing mantises (Cernomantodea) was inferred as Early Cretaceous (119 Ma, 95% CI: 110–129 Ma). The molecular dating results indicated that the hearing organ in mantises did not arise in response to bat predation. Our study provides a robust framework for further evolutionary comparative studies of mantises.</p>
Figure 21 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 21. Dorsoposterior and lateral views of mesosoma. A, Holophris huberi; B, Parnopes grandior; C, E, Allocoelia capensis (Smith) (NHMUK 010576396); D, Caenochrysis nigropolita (Bischoff); F, Allocoelia emarginata Edney (NHMUK 010576397). Scale bars: 0.2 mm (A); 0.5 mm (B, D); 1 mm (C, E, F). Images of A. capensis and A. emarginata available under Creative Commons License 4.0. Natural History Museum: data.nhm.ac.uk. Arrowheads indicate morphological conditions coded as character-states.
Figure 19 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 19. Dorsal view of mesosoma. The axillae are colour-marked. A, Parnopes grandior (Pallas), male; B, Exallopyga guatemalensis (Cameron), female; C, Allocoelia emarginata Edney, female (NHMUK 010576397); D, Caenochrysis crotonis (Ducke), female. Scale bars (A, B, D): 0.5 mm; (C): 1 mm. Image of A. emarginata available under Creative Commons License 4.0. Natural History Museum: data.nhm.ac.uk. Arrowheads indicate morphological conditions coded as character-states.
Figure 18 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 18. Comparative phylogenetic hypotheses on the evolutionary relationships among tribes of the Chrysidinae cuckoo wasps obtained from different sources. A, B, cladistic morphology-based hypotheses. C, D, molecularbased hypotheses. The uncertain position of Allocoeliini is represented as '?' (the placement of this taxon was not inferred by Niehuis & Wägele, 2004).
Figure 17 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 17. Scanning electron microscopy images of morphological structures of head. A, clypeus and mandibles of Adelphe brasiliensis, male; B, clypeus of Pleurochrysis postica (Brullé); C, clypeus and mandibles of Elampus gayi (Spinola), female; D, clypeus and mandibles of Holopyga wagnerella du Buysson, female; E–H, anterior surface of mandibles: E, Caenochrysis nigropolita (Bischoff), female; F, Hedychridium periotoi Lucena, female; G, Muesebeckidium paraensis (Ducke), female; H, H. wagnerella, female. I–K, C. nigropolita, female, frontal view of scapal basin with the facial fovea shown in amplified views. Arrowheads indicate morphological conditions coded as character-states.
Figure 14 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 14. Lateral view of female metasoma. A, Cleptidea sp.; B, Adelphe sp.; C, Exallopyga guatemalensis (Cameron); D, Spintharina vagans Radoszkowski; E, Exochrysis spinigera (Spinola); F, Neochrysis carina (Brullé); G, Ipsiura myops (du Buysson); H, Chrysis brasiliensis Brullé; I, Stilbum cyanurum (Förster). Scale bars (A, B): 1 mm; (C–I): 0.5 mm.
Figure 12 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 12. Part of the maximum credibility Bayesian tree obtained from a combined analysis employing a relaxed morphological clock model with tip-dating. Phylogenetic relationships among representatives of Chrysidinae: Chrysidini partim. Character-state transformations (ChN, character; ChS, character state) are colour-coded with tagma as represented in the diagram on the bottom, and are depicted as solid (unequivocal changes) or empty (reversed or multiple changes) charts; mesosomal characters derived from legs and wings are depicted as rectangle and hexagon portrayals respectively; slow changes (DelTran optimization) are indicated by '+'.
Figure 10 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 10. Part of the maximum credibility Bayesian tree obtained from a combined analysis employing a relaxed morphological clock model with tip-dating. Phylogenetic relationships among representatives of Chrysidinae: Parnopini and Allocoeliini. Character state transformations (ChN, character; ChS, character state) are colour-coded with tagma as represented in the diagram on the top, and are depicted as solid (unequivocal changes) or empty (reversed or multiple changes) charts; mesosomal characters derived from legs and wings are depicted as rectangle and hexagon portrayals respectively; slow changes (DelTran optimization) are indicated by '+'. Fossil taxa are indicated by daggers. Phylogenetic relationships among Chrysidini species (Clade 5) are shown in detail in Figures 11–12.
Figure 8 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 8. Part of the maximum credibility Bayesian tree obtained from a combined analysis employing a relaxed morphological clock model with tip-dating. Phylogenetic relationships among representatives of Loboscediliinae and Amiseginae. Character-state transformations (ChN, character; ChS, character state) are colour-coded with tagma as represented in the diagram on the bottom, and are depicted as solid (unequivocal changes) or empty (reversed or multiple changes) charts; mesosomal characters derived from legs and wings are depicted as rectangle and hexagon portrayals respectively; slow changes (DelTran optimization) are indicated by '+'. Fossil taxa are indicated by daggers.
Figure 7 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 7. Part of the maximum credibility Bayesian tree obtained from a combined analysis employing a relaxed morphological clock model with tip-dating. Phylogenetic relationships among representatives of Cleptinae and extinct Chrysididae taxa. Character-state transformations (ChN, character; ChS, character state) are colour-coded with tagma as represented in the diagram on the bottom, and are depicted as solid (unequivocal changes) or empty (reversed or multiple changes) charts; mesosomal characters derived from legs and wings are depicted as rectangle and hexagon portrayals respectively; slow changes (DelTran optimization) are indicated by '+'. Fossil taxa are indicated by daggers. Phylogenetic relationships among other subfamilies of Chrysididae (Clades 2 and 3) are shown detail in Figures 8–12.
Figure 6. Maximum credibility Bayesian tree obtained from a in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 6. Maximum credibility Bayesian tree obtained from a combined analysis of a partitioned dataset of 300 morphological characters employing a relaxed morphological clock model with tip-dating. Character-state transformations (ChN, character; ChS, character state) are colour-coded with tagma as represented in the diagram on the bottom, and are depicted as solid (unequivocal changes) or empty (reversed or multiple changes) charts; mesosomal characters derived from legs and wings are depicted as rectangle and hexagon portrayals respectively; slow changes (DelTran optimization) are indicated by '+'. Fossil taxa are indicated by daggers. Phylogenetic relationships among Chrysididae (Clade 1) are shown in detail in Figures 7–12.
Figure 4 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 4. Chronogram for Chrysidinae, partim (Chrysididae) derived from a combined Bayesian analysis of a partitioned dataset of 300 morphological characters employing a relaxed morphological clock model with tip-dating. The chrysidine clade connects to the remaining tree of Chrysididae in Figure 3; phylogenetic relationships among the species of Chrysidini are shown in the Figure 5. Branch lengths are drawn proportional to time from the present (timescale on the bottom), highest posterior density (HPD) 95% intervals for the ages of select nodes are indicated by horizontal blue bars, and node support values correspond to Bayesian posterior probabilities. Lowercase letters indicate clades of major interest (discussed in the text) with their respective estimated ages. Fossil taxa are indicated by daggers.
Figure 5 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 5. Chronogram for Chrysidini (Chrysididae: Chrysidinae) derived from a combined Bayesian analysis of a partitioned dataset of 300 morphological characters employing a relaxed morphological clock model with tip-dating. The clade herein represented connects to the remaining tree of Chrysidinae in Figure 4. Branch lengths are drawn proportional to time from the present (timescale on the bottom), highest posterior density (HPD) 95% intervals for the ages of selected nodes are indicated by horizontal blue bars, and node support values correspond to Bayesian posterior probabilities. Lowercase letters indicate clades of major interest (discussed in the text) with their respective estimated ages. Fossil taxa are indicated by daggers.
Figure 13 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 13. Maximum credibility Bayesian dated tree calculated for the Chrysididae and distribution of terminals in biogeographic divisions of the world. The charts on tips represent the true geographical range for the genus or lineage being considered. Widespread taxa are represented on tips by multicolour charts. The pruned tree was obtained from a maximum credibility Bayesian dated tree considering all compatible groups (contype = allcompat in MrBayes). Groups of species were combined into lineages representing monophyletic genera or other taxon combinations. Monophyletic groups are represented by their genus names only. Non-monophyletic taxa are represented multiple times. Biogeographic reconstruction of the history of Chrysididae was conducted using the DEC model as implemented in BioGeoBEARS. Pie charts at nodes show the relative probability of the possible states (areas or combinations of areas) indicated by asterisk those higher than 50%; combinations of areas are indicated by grey slices; black slices represent a fraction of the reconstructions with high ambiguity.
Figure 11 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 11. Part of the maximum credibility Bayesian tree obtained from a combined analysis employing a relaxed morphological clock model with tip-dating. Phylogenetic relationships among representatives of Chrysidinae: Chrysidini partim. Character-state transformations (ChN, character; ChS, character state) are colour-coded with tagma as represented in the diagram on the bottom, and are depicted as solid (unequivocal changes) or empty (reversed or multiple changes) charts; mesosomal characters derived from legs and wings are depicted as rectangle and hexagon portrayals respectively; slow changes (DelTran optimization) are indicated by '+'. Fossil taxa are indicated by daggers. Phylogenetic relationships among other Chrysidini species (Clades 6 and 7) are shown in detail in Figure 12.
Figure 2 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 2. Comparison between phylogenetic hypotheses for extant groups of Chrysididae and closely related taxa of Chrysidoidea: A, summary of morphology-based hypotheses (Kimsey & Bohart, 1991; Carpenter, 1999; Lucena & Melo, 2018; Melo & Lucena, 2020); B, summary of the DNA-based hypothesis by Pauli et al. (2019, 2021). The phylogenetic position of Loboscelidiinae (Chrysididae) is indicated with a question mark because it was not inferred by Pauli et al. (2019, 2021). Fossil taxa not included in the molecular analyses are represented by dashed lines.
Figure 1 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 1. Summary of the phylogenetic relationships and valid genera of Chrysididae based on Kimsey & Bohart (1991) with recent amendments. The placement of Kimseya and †Eochrysis are considered herein as uncertain within the Chrysidinae. The main groups being considered in the family are colour-coded. Fossil taxa are indicated by daggers.
Figure 22 in Morphology and Bayesian tip-dating recover deep Cretaceous-age divergences among major chrysidid lineages (Hymenoptera: Chrysididae)
Figure 22. Scanning electron microscopy images of ventral and dorsal views of metasomas, and posterior view of mesosomas. Metasomal carina is colour-indicated. A, Holopyga luzulina Dahlbom, female, ventral view of metasoma, higher magnification of the anterior area of metasoma is shown in C. B, Exochrysis leucostigma (Mocsáry), male, ventral view of metasoma, higher magnification of the anterior area of metasoma is shown in D. Dorsal views of T1: E, Exallopyga guatemalensis (Cameron), female; F, Neochrysis inseriata (Mocsáry), female. Posterior view of mesosomas: G, Holopyga wagnerella du Buysson, female; H, Caenochrysis paranaca (Linsenmaier), female. Arrowheads indicate morphological conditions coded as character-states.
FIGURE 2 in Sixteen vetted fossil calibrations for divergence dating of Charadriiformes (Aves, Neognathae)
FIGURE 2. Phylogram of alcid relationships showing calibrated nodes 7-15 (modified from Smith, 2011a, figure 1.26). Numbered nodes in red correspond to the following calibrations: (8) divergence of Alcidae from Stercorariidae; (9) divergence of Aethiini from Fraterculini; (10) divergence of Fratercula arctica from Fratercula corniculata; (11) divergence of Cepphus carbo from Cepphus columba; (12) divergence of Synthliboramphus hypoleucus from Synliboramphus craveri;divergence of Synthliboramphus hypoleucus from Synthliboramphus craveri; (13) divergence of Brachyramphus marmoratus from Brachyramphus brevirostris; (14) divergence of Alle alle from Uria; (15) divergence of Uria lomvia from Uria aalge; (16) divergence of Alca torda from Pinguinus impennis.
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