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opennotspecifiedSep 2023View details →

Fig. 1 in The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps

Fig. 1. Comparison of properties of the analysed datasets. Datasets (AHE414 and UCEs) are described in Table 1. For each panel, letters above box plots reflect pairwise comparisons of marginal means estimated from the best-fit models; distributions sharing a letter do not differ significantly. Points: raw data (Table S2a). In (e), saturation was assessed by calculating the R2 of the linear regression of uncorrected p-distances against inferred distances in individual gene trees. Highest R2 are for least saturated loci. The scale of the Y axis is reversed to better show decrease in saturation. (f) The convergence of trees as saturation decreases. The Y axis shows the relative RF distance between pairs of trees obtained with either the combined exons or the combined UCEs. The X axis show the absolute value of the difference between the medians of the R2 of the linear regression of uncorrected p-distances against inferred distances in gene trees that were combined to get the compared trees [cf. (e)]. Four comparisons were performed in each case as datasets were analysed with and without partitioning.

opennotspecifiedSep 2023View details →

Fig. 5 in The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps

Fig. 5. Global historical biogeography of Chalcidoidea and new classification. The chronogram obtained from the complete set of ingroup taxa is illustrated. The previous classification is used to annotate tips (four letter prefixes; see also Table S1 for complete information on sampling) with successive grey and white boxes grouping the tip labels. The new familial classification from Burks et al. (2022) is shown to the right. For clarity, ancestral ranges are given only up to family level and only for the BAYEAREALIKE + J model (which was selected by AICc). All inferences of ancestral ranges are provided in Fig. S5. Inferences of ancestral ranges were conducted with only one specimen per genus as shown with brackets that connect tips. Current distribution of genera is shown with coloured boxes at tips. Sampling area of specimens is indicated in tip labels. NEO = Neotropical; NEA = Nearctic; AFR = Afrotropical; PAL = Palaearctic; ORI = Oriental; AUS = Australasian. UKN = Unknown when collection data are unavailable. Stars indicate that specimens were sampled in areas where species was introduced or not yet cited. Sampling area for the specimen used for sequencing exons is listed first, sampling area for the specimen used for sequencing UCEs is listed second; n.a. is used when no specimen was sequenced and only one sampling area is reported when exons and UCEs were obtained from specimens sampled in the same areas (or from the same specimen). Unless specified, nodes are supported by SHaLRT ≥80%, UFBoot ≥95% and sCF ≥34.3 (minimum support for a family that is well defined morphologically, Trichogrammatidae). Nodes with a grey circle are supported by SHaLRT <80% or UFBoot <95%; nodes with a black circle are supported by SHaLRT <80% and UFBoot <95%; nodes with a black triangle are supported with sCF <34.3. Images on the left of tentative family names are all at the same scale. Images on the right of tentative family names have been magnified. Photos ©K. Bolte (Baeomorphidae); ©J.-Y. Rasplus (all others).

opennotspecifiedSep 2023View details →

Fig. 4 in The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps

Fig. 4. The Chalcidoidea bush of life. (a) IQ-TREE tree obtained from the combined exonsAA+UCEs90-25 datasets (see also Fig. S1). Monophyletic families are in grey, para- or polyphyletic families are in colour. Higher level groups/clades discussed in text are highlighted with boxes. Statistical support for backbone nodes are shown with single (SH-aLRT ≧80% or UFboot ≧95%) or double stars (SH-aLRT ≧80% and UFboot ≧95%). (b) Contribution of the exonsAA and UCEs90-25 datasets to the combined tree. Gene concordance factor (gCF); gene discordance factor due to polyphyly (gDFP); site concordance factor averaged over 100 quartets (sCF). Points: raw data (Table S2d). (c) Comparison of branch length for the backbone nodes and other ingroup nodes. Points: raw data (Table S2c). For (b) and (c), stars above box plots indicate statistical significance: ns, p> 0.05; ***, p ≤ 0.001; ****, p ≤ 0.0001. (d) Correlation between node age and sCF (outgroups excluded). Points: raw data (Table S2e); line: regression curve for the best-fit model (log linear model; p <2.2e—16).

Fig. 6 in The explosive radiation, intense host-shifts and long-term failure to speciate in the evolutionary history of the feather mite genus Analges (Acariformes: Analgidae) from European passerines

Fig. 6. The co-phylogenetic scenarios revealed by JANE analysis. Thin black lines are the Analges phylogenetic tree, wide grey lines are the bird tree. The legend shows the cost of each event (in parentheses) near every co-phylogenetic event and the number of reconstructed events. A, original analysis with the full set of taxa in multi-host Analges–bird associations.? – after speciation, the ancestral species still exists. B, dated best-cost scenarios of the multi-host associations reduced to a single host species and supplemented by spread events for remaining host species. Clades in multi-host species remained as in the original analysis, i.e. originated by failure to speciate. The circles near Analges species names designate the components of host nests: black circles, fine feathers and/or down in nest material; white circles, no feathers in nest material (after Gotzman & Jablonski, 1972 and Beuch, 2013).

Fig. 5 in The explosive radiation, intense host-shifts and long-term failure to speciate in the evolutionary history of the feather mite genus Analges (Acariformes: Analgidae) from European passerines

Fig. 5. Character tracing of two key morphological characteristics of Analges: finger-like process on tarsi III in males (A) and chelate hypertrophied legs III in heteromorph males (B). Changes were traced onto the final tree (Fig. 4) using likelihood asymmetrical two-parameter Markov model with differently estimated forward/backward rates of character state changes.

Fig. 4 in The explosive radiation, intense host-shifts and long-term failure to speciate in the evolutionary history of the feather mite genus Analges (Acariformes: Analgidae) from European passerines

Fig. 4. Diversification of Analges through time. A, dated maximum clade credibility tree revealed by BEAST analysis from concatenated COI, 16S and 28S sequences for Analges species and their outgroups. Intensity of node colouration designates PP of Bayesian analysis. The chronostratigraphic scale is given with absolute geological ages (MYA, million years ago). The node bars indicate credibility intervals (± 95% highest posterior densities HPD). Two columns of coloured squares on the right designate two taxonomic hypotheses of intrageneric groupings. The category 'ungrouped' describe male Analges without both chelate legs III and finger-like processes on tarsi III. B, lineages through time (LTT) plot for Analges. The upturn around 23 Mya reflects an acceleration in the rate of speciation which coincides with the origin of the crown in the Analges clade.

Fig. 3 in The explosive radiation, intense host-shifts and long-term failure to speciate in the evolutionary history of the feather mite genus Analges (Acariformes: Analgidae) from European passerines

Fig. 3. Phylogenetic conflict in the BI post-burnin trees reconstructed from concatenated sequences of COI, 16S and 28S as shown by consensus network analyses for threshold values 0.3 (A) and 0.012 (B). The hypothesized Analges corvinus–A. sturninus clade is depicted in red, the hypothesized Analges sp.n. 6–A. sturninus clade is depicted in blue. The numbers near splits are confidence values for alternate hypotheses.

Fig. 1 in The explosive radiation, intense host-shifts and long-term failure to speciate in the evolutionary history of the feather mite genus Analges (Acariformes: Analgidae) from European passerines

Fig. 1. Morphological characteristics applied in two different intrageneric groupings in the Analges genus. A, general view of male, Analges corvinus, ventral side; B, hypertrophied leg III in males of the passerinus species group, A. passerinus, dorsal side; C, hypertrophied leg III in males of the chelopus species group, A. spiniger, ventral side; D, male tarsus III with ventral finger-like process bearing seta w in Analgopsis subgenus, A. poppei, dorsal side; E, male tarsus III lacking the ventral process in Analges subgenus, A. corvinus, ventral side.

Fig. 2 in The explosive radiation, intense host-shifts and long-term failure to speciate in the evolutionary history of the feather mite genus Analges (Acariformes: Analgidae) from European passerines

Fig. 2. Neighbour-joining tree with sequence groups of putative Analges species recovered by automatic barcode gap discovery from COI barcode sequences.

opencc-zeroJun 2022View details →

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Data from: Compensatory adaptation and diversification subsequent to evolutionary rescue in a model adaptive radiation

Biological populations may survive lethal environmental stress through evolutionary rescue. The rescued populations typically suffer a reduction in growth performance and harbour very low genetic diversity compared with their parental populations. The present study addresses how population size and within-population diversity may recover through compensatory evolution, using the experimental adaptive radiation of bacterium Pseudomonas fluorescens. We exposed bacterial populations to an antibiotic treatment; and then imposed a one-individual-size population bottleneck on those surviving the antibiotic stress. During the subsequent compensatory evolution, population size increased and leveled off very rapidly. The increase of diversity was of slower paces and persisted longer. In the very early stage of compensatory evolution, populations of large sizes had a greater chance to diversify; however, this productivity-diversification relationship was not observed in later stages. Population size and diversity from the end of the compensatory evolution was not contingent on initial population growth performance. We discussed the possibility that our results be explained by the emergence of a "holey" fitness landscape under the antibiotic stress.

opennotspecifiedMay 2015View details →

Fig. 3 in The hypothesis of adaptive radiation in evolutionary biology: hard facts about a hazy concept

Fig. 3 Systematic characteristics of the groups having possibly radiated. a Number of case studies (potentially several case studies per article) recorded for each category of organism: angiosperms (n =210), nonangiosperm terrestrial plants (n = 36), "algae", non-terrestrial chlorophyllian lineages (n = 9), tetrapods (n = 381), non-tetrapod vertebrates (n =121), hexapods (n =153), non-hexapod invertebrates (n = 90), fungi, Eumycetes (n =22), non-metazoan heterotrophic eukaryotes

opennotspecifiedMay 2015View details →

Fig. 1 in The hypothesis of adaptive radiation in evolutionary biology: hard facts about a hazy concept

Fig. 1 Various metrics relative to the study of adaptive radiations over the 2003–2012 time period. a Number of articles extracted from the Web of Science™ database, after the third step of our search procedure (see the "Material and methods" section for details), for each journal and for each year. b Percentage of articles that examined the hypotheses of radiation

opennotspecifiedMay 2015View details →

Fig. 5 in The hypothesis of adaptive radiation in evolutionary biology: hard facts about a hazy concept

Fig. 5 Features of the insular systems investigated in studies about radiations between 2003 and 2012. Numbers and percentages are relative to case studies (potentially several case studies per article). a Location of the possible radiation. b Percentage of case studies for each of the island types identified in the dataset. c The Suski Inselberg, Maripasoula, French Guiana (credit: Corinne Sarthou). d Number of

Figure 2 in Evolutionary origins of the lampriform pelagic radiation

Figure 2. Strict consensus topology of lampriform relationships based on morphology. Strict consensus of 355 most parsimonious trees inferred from analysis of the morphological dataset using TNT v.1.5. Key clades are labelled. Numbers indicate bootstrap supports. Nodes without numbers are supported by bootstrap values of less than 60. Fish illustrations are by C.D.B., after Davesne et al. (2016), Carnevale and Bannikov (2018), Underkoffler et al. (2018), FishBase.se, Phylopic.org (public domain silhouettes), and those in the public domain.

Figure 5 in Evolutionary origins of the lampriform pelagic radiation

Figure 5. Time-calibrated Bayesian phylogeny of Lampriformes based on nuclear sequence data and fossil tip-calibrations. Maximum clade credibility tree generated from analysis of the tip-dated nuclear gene sequence dataset in BEAST 2.6.6. Key clades are labelled. Grey bars indicate 95% HPD intervals. Numbers indicate posterior values (those less than 0.85 or values associated with forced monophyletic constraints not included). Fish illustrations are by C.D.B., after Davesne et al. (2016), Carnevale and Bannikov (2018), Underkoffler et al. (2018), FishBase.se, Phylopic.org (public domain silhouettes), and those in the public domain.

Figure 1 in Evolutionary origins of the lampriform pelagic radiation

Figure 1. Previous hypotheses of lampriform phylogeny. Phylogenies presented in (a) Oelschläger (1983), (b) Olney et al. (1993), and (c) Martin (2015). Silhouettes from Phylopic.org or created from public domain images.

Figure 4 in Evolutionary origins of the lampriform pelagic radiation

Figure 4. Bayesian phylogeny of Lampriformes based on nuclear sequence data. Phylogeny generated in MrBayes v.3.2. Numbers indicate posterior support values. Fish illustrations are by C.D.B., after Underkoffler et al. (2018), FishBase.se, Phylopic.org (public domain silhouettes), and those in the public domain.

Figure 3 in Evolutionary origins of the lampriform pelagic radiation

Figure 3. Time-calibrated Bayesian phylogeny of Lampriformes based on morphology. Maximum clade credibility tree generated from analysis of the morphological dataset in BEAST 2.6.6. Key clades are labelled. Grey bars indicate 95% highest posterior density intervals of the age estimates. Numbers indicate posterior values (those less than 0.60 not shown). Fish illustrations are by C.D.B., after Davesne et al. (2016), Carnevale and Bannikov (2018), Underkoffler et al. (2018), FishBase.se, Phylopic.org (public domain silhouettes), and those in the public domain.

opencc-zeroDec 2022View details →

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Evolutionary radiation in canids following continental colonizations

Colonization of a new environment may trigger a remarkable radiation process, defined as an accelerated accumulation of species in a short period of time. However, how often colonization events trigger such radiations is still an open question. We studied the worldwide dispersal of the subfamily Caninae to investigate whether the invasion of new continents resulted in a great increase in species diversification. We used a combination of phylogenetic analyses and ancestral area reconstructions to estimate ancestral ranges of 56 extant and extinct species of Caninae, as well as variation in speciation and extinction rates through time and across clades. Our findings indicate that canids experienced a remarkable radiation event when lineages were able to reach Eurasia and South America around 11 million years ago. This large number of species arising in a short period of time suggests that canids experienced ecological opportunity events within the new areas, implying that the differences in the ecological settings between continents, and size variation among Canidae and other carnivores may be responsible for the variation in clade dynamics. We suggest that the advance of grasslands and the new herbivorous fauna that came with it were the major forces responsible for the diversification of wolves in North America. On the other hand, empty niches and the absence of competitors can explain the success of canids in Africa and South America. We argue that interaction with other carnivores probably also affected the diversification dynamics of canids.