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13 results for “ghost lineages”
Genomic landscape of introgression from the ghost lineage in a gobiid fish uncovers the generality of forces shaping hybrid genomes
<p>Extinct lineages can leave legacies in the genomes of extant lineages through ancient introgressive hybridization. The patterns of genomic survival of these extinct lineages provide insight into the role of extinct lineages in current biodiversity. However, our understanding of the genomic landscape of introgression from extinct lineages remains limited due to challenges associated with locating the traces of unsampled "ghost" extinct lineages without ancient genomes. Herein, we conducted population genomic analyses on the East China Sea (ECS) lineage of <em>Chaenogobius annularis</em>, which was suspected to have originated from ghost introgression, with the aim of elucidating its genomic origins and characterizing its landscape of introgression. By combining phylogeographic analysis and demographic modeling, we demonstrated that the ECS lineage originated from ancient hybridization with an extinct ghost lineage. Forward simulations based on the estimated demography indicated that the statistic <em>γ</em> of the HyDe analysis can be used to distinguish the differences in local introgression rates in our data. Consistent with introgression between extant organisms, we found reduced introgression from extinct lineage in regions with low-recombination rates and with functional importance, thereby suggesting a role of linked selection that has eliminated the extinct lineage in shaping the hybrid genome. Moreover, we identified enrichment of repetitive elements in regions associated with ghost introgression, which was hitherto little-known but was also observed in the reanalysis of published data on introgression between extant organisms. Overall, our findings underscore the unexpected similarities in the characteristics of introgression landscapes across different taxa, even in cases of ghost introgression.</p>
Genomic landscape of introgression from the ghost lineage in a gobiid fish uncovers the generality of forces shaping hybrid genomes
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Data from: Major radiations in the evolution of caviid rodents: reconciling fossils, ghost lineages, and relaxed molecular clocks
BACKGROUND: Caviidae is a diverse group of caviomorph rodents that is broadly distributed in South America and is divided into three highly divergent extant lineages: Caviinae (cavies), Dolichotinae (maras), and Hydrochoerinae (capybaras). The fossil record of Caviidae is only abundant and diverse since the late Miocene. Caviids belongs to Cavioidea sensu stricto (Cavioidea s.s.) that also includes a diverse assemblage of extinct taxa recorded from the late Oligocene to the middle Miocene of South America ("eocardiids"). RESULTS: A phylogenetic analysis combining morphological and molecular data is presented here, evaluating the time of diversification of selected nodes based on the calibration of phylogenetic trees with fossil taxa and the use of relaxed molecular clocks. This analysis reveals three major phases of diversification in the evolutionary history of Cavioidea s.s. The first two phases involve two successive radiations of extinct lineages that occurred during the late Oligocene and the early Miocene. The third phase consists of the diversification of Caviidae. The initial split of caviids is dated as middle Miocene by the fossil record. This date falls within the 95% higher probability distribution estimated by the relaxed Bayesian molecular clock, although the mean age estimate ages are 3.5 to 7 Myr older. The initial split of caviids is followed by an obscure period of poor fossil record (refered here as the Mayoan gap) and then by the appearance of highly differentiated modern lineages of caviids, which evidentially occurred at the late Miocene as indicated by both the fossil record and molecular clock estimates. CONCLUSIONS: The integrated approach used here allowed us identifying the agreements and discrepancies of the fossil record and molecular clock estimates on the timing of the major events in cavioid evolution, revealing evolutionary patterns that would not have been possible to gather using only molecular or paleontological data alone.
Supplementary material 2 from: Wesener T, Voigtländer K, Decker P, Oeyen JP, Spelda J (2016) Barcoding of Central European Cryptops centipedes reveals large interspecific distances with ghost lineages and new species records from Germany and Austria (Chilopoda, Scolopendromorpha). ZooKeys 564: 21-46. https://doi.org/10.3897/zookeys.564.7535
Uncorrected P-Distance : Explanation note: Uncorrected P-Distance between the 66 analyzed specimens.
Data from: Ecological correlates of ghost lineages in ruminants
Integration between phylogenetic systematics and paleontological data has proved to be an effective method for identifying periods that lack fossil evidence in the evolutionary history of clades. In this study we aim to analyze whether there is any correlation between various ecomorphological variables and the duration of these underrepresented portions of lineages, which we call ghost lineages for simplicity, in ruminants. Analyses within phylogenetic (Generalized Estimating Equations) and non-phylogenetic (ANOVAs and Pearson correlations) frameworks were performed on the whole phylogeny of this suborder of Cetartiodactyla (Mammalia). This is the first time ghost lineages are focused in this way. To test the robustness of our data, we compared the magnitude of ghost lineages among different continents and among phylogenies pruned at different ages (4, 8, 12, 16, and 20 Ma). Differences in mean ghost lineage were not significantly related to either geographic or temporal factors. Our results indicate that the proportion of the known fossil record in ruminants appears to be influenced by the preservation potential of the bone remains in different environments. Furthermore, large geographical ranges of species increase the likelihood of preservation.
Data from: Ecological correlates of ghost lineages in ruminants
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Data from: Major radiations in the evolution of caviid rodents: reconciling fossils, ghost lineages, and relaxed molecular clocks
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Supplementary material 1 from: Wesener T, Voigtländer K, Decker P, Oeyen JP, Spelda J (2016) Barcoding of Central European Cryptops centipedes reveals large interspecific distances with ghost lineages and new species records from Germany and Austria (Chilopoda, Scolopendromorpha). ZooKeys 564: 21-46. https://doi.org/10.3897/zookeys.564.7535
Full specimen information : Explanation note: Full specimen information.
Figure 4 from: Wesener T, Voigtländer K, Decker P, Oeyen JP, Spelda J (2016) Barcoding of Central European Cryptops centipedes reveals large interspecific distances with ghost lineages and new species records from Germany and Austria (Chilopoda, Scolopendromorpha). ZooKeys 564: 21-46. https://doi.org/10.3897/zookeys.564.7535
Figure 4 - Distribution map of all successfully sequenced Central European specimens of Cryptops parisi. Different colours mark the three different clades. Yellow = Cryptops parisi sensu stricto; blue = Cryptops parisi sebini; green = Cryptops parisi lineage 3 (potentially Cryptops cf. hortensis sensu Pichler 1987).
Figure 3 from: Wesener T, Voigtländer K, Decker P, Oeyen JP, Spelda J (2016) Barcoding of Central European Cryptops centipedes reveals large interspecific distances with ghost lineages and new species records from Germany and Austria (Chilopoda, Scolopendromorpha). ZooKeys 564: 21-46. https://doi.org/10.3897/zookeys.564.7535
Figure 3 - Frequency distribution of pairwise intraspecific (blue) and interspecific (red) distances. All lineages of Cryptops parisi treated as one species, Cryptops parisi sensu lato. Basic table see Suppl. material 1.
Figure 2 from: Wesener T, Voigtländer K, Decker P, Oeyen JP, Spelda J (2016) Barcoding of Central European Cryptops centipedes reveals large interspecific distances with ghost lineages and new species records from Germany and Austria (Chilopoda, Scolopendromorpha). ZooKeys 564: 21-46. https://doi.org/10.3897/zookeys.564.7535
Figure 2 - Maximum likelihood tree under the GTR+G+I model, 1000 bootstrap replicates. Colours and symbols correspond to Maps (Figs 1, 4). Country of origin given after specimen number: AT = Austria; DE = Germany; GB = Wales; HR = Croatia; IT = Italy; SL = Slovenia. Photograph shows a specimen of Cryptops parisi s.s. from Breckerfeld (photo A. Steiner), western Germany. For full data on all specimens, see Table 1.
Figure 1 from: Wesener T, Voigtländer K, Decker P, Oeyen JP, Spelda J (2016) Barcoding of Central European Cryptops centipedes reveals large interspecific distances with ghost lineages and new species records from Germany and Austria (Chilopoda, Scolopendromorpha). ZooKeys 564: 21-46. https://doi.org/10.3897/zookeys.564.7535
Figure 1 - Distribution map of all successfully sequenced Central European specimens of Cryptops. Numbers refer to each specimen (see Table 1). Symbols and colours denote species. Blue rectangle = Cryptops parisi; red circle = Cryptops anomalans; green triangle = Cryptops hortensis; brown diamond = Cryptops croaticus; orange cross = Cryptops umbricus; light blue, orange, and yellow symbols mark undetermined Cryptops species.
Figure 5 from: Wesener T, Voigtländer K, Decker P, Oeyen JP, Spelda J (2016) Barcoding of Central European Cryptops centipedes reveals large interspecific distances with ghost lineages and new species records from Germany and Austria (Chilopoda, Scolopendromorpha). ZooKeys 564: 21-46. https://doi.org/10.3897/zookeys.564.7535
Figure 5 - Frequency distribution of pairwise intraspecific (blue) and interspecific (red) distances. The three lineages of Cryptops parisi treated as different species. Basic table see Suppl. material 1.
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