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26 results for “Miocene radiation”
Data set: Australia's hidden radiation - phylogenomic analysis reveals rapid Miocene radiation of blindsnakes
<p>This repository contains the additional raw data to accompany our paper entitled "Australia’s hidden radiation: phylogenomic analysis reveals rapid Miocene radiation of blind snakes."</p> <p>This project is part of the AusARG Initiative funded by BioPlatforms Australia.</p> <p>Raw sequences data can be downloaded from the BioPlatforms downloads portal: https://data.bioplatforms.com/dataset?q=ticket%3ABPAOPS-1196</p> <p><strong>Information about files</strong></p> <ol> <li>ASTRAL_tree_SqCL_AHE.tre - output from ASTRAL-III just with SqCL data + outgroups</li> <li>ASTRAL_tree_SqCL_AHE_Ramphotyphlops.tre - same with above but also including additional <em>Ramphotyphlops </em>genes.</li> <li>mcmctree_1.txt - mcmcfile output from MCMCTree analysis using all SkewT or SkewNormal distribution priors.</li> <li>mcmctree_2.txt - mcmcfile output from MCMCTree analysis using SkewT, SkewNormal, and cauchy distribution priors. **This is the tree used in our publication**</li> <li>mcmctree_strategy1.tre - output phylogeny 1</li> <li>mcmctree_strategy2.tre - output phylogeny 2</li> <li>IQTREE_gcf_scf.nex - gene concordance and site factors for mcmctree_strategy2.tre</li> </ol> <p>tree_data/ folder contains concatenated gene trees (IQTREE) and corresponding shortcut coalescent method (ASTRAL-III) tree.</p> <p>Should there be questions regarding the code and data set, please contact the corresponding author.</p>
FIGURE 8 in New Miocene fossil taxa illuminate the evolution and paleobiogeography of the Ponto-Caspian gammaroid amphipod radiation
FIGURE 8 Specimen (inventory No. 8244, Vlădiceni quarry) showing a resemblance to extant genera Chaetogammarus and Litorogammarus. Scale bar = 1 mm.
FIGURE 7 in New Miocene fossil taxa illuminate the evolution and paleobiogeography of the Ponto-Caspian gammaroid amphipod radiation
FIGURE 7 †Eogmelina moldavica gen. et sp. nov. next to a fossilized alga (inventory No. 8240, Vlădiceni quarry). Scale bar = 5 mm. Downloaded from Brill.com 06/21/2024 06:25:54PM via Open Access. This is an open access article distributed under the terms of the CC BY 4.0 license. https://creativecommons.org/licenses/by/4.0/
FIGURE 5 in New Miocene fossil taxa illuminate the evolution and paleobiogeography of the Ponto-Caspian gammaroid amphipod radiation
FIGURE 5 †Eogmelina moldavica gen. et sp. nov. On the right are interpretative drawings of the corresponding fossils on the left. (A) Holotype male and paratype female (inventory No. 8236, Vlădiceni quarry), (B) male (inventory No. 8237, Vlădiceni quarry), (C) female (inventory No. 8238, Iași City), (D) female (inventory No. 8239, Vlădiceni quarry). Scale bars = 1 mm. Abbreviations: A = antenna; B = basis; C = coxa; G = gnathopod; H = head; P = pereonite; PL = pleonite; PP = pereopod; U = urosomite; UP = uropod; T = telson.
FIGURE 6 in New Miocene fossil taxa illuminate the evolution and paleobiogeography of the Ponto-Caspian gammaroid amphipod radiation
FIGURE 6 †Eogmelina prisca gen. et sp. nov. On the right are interpretative drawings of the corresponding fossils on the left. (A) Holotype male (inventory No. 8241, Vlădiceni quarry), (B) paratype male (inventory No. 8242, Iași City), (C) disarticulated remains of unknown sex (inventory No. 8243, Vlădiceni quarry). Scale bars = 1 mm. Abbreviations: A = antenna; B = basis; C = coxa; G = gnathopod; H = head; P = pereonite; PL = pleonite; PP = pereopod; U = urosomite; UP = uropod; T = telson.
FIGURE 4 in New Miocene fossil taxa illuminate the evolution and paleobiogeography of the Ponto-Caspian gammaroid amphipod radiation
FIGURE 4 Morphological diversity of extant and fossil Ponto-Caspian gammaroids based on 43 morphometric measurements. (A) PCA plot depicting the morphospace occupation along the first two axes. Extant non-monotypic genera are shown with dimmed colors (dots or convex hulls if n> 2 species) while monotypic genera are shown with a gray square. Fossil taxa are shown with colored stars that are numbered according to species (see legend on lower left). Extreme morphologies are exemplified by drawings. (B) Biplot of variables along the first two PCA axes. C) A 3D PCA indicating morphospace occupation of fossils (colored triangles) and extant (gray dots) taxa within the first three axes.
FIGURE 3 in New Miocene fossil taxa illuminate the evolution and paleobiogeography of the Ponto-Caspian gammaroid amphipod radiation
FIGURE 3 Multivariate clustering (Ward's method) based on a Gower-transformed matrix of 114 morphological characters. The heat map represents a pairwise matrix of Euclidean distances among taxa. High similarity is shown with blue while low similarity with red. Green dots at nodes in the dendrograms indicate wellsupported groups (bootstrap values> 70%). The fossil clade is highlighted with orange and dagger symbol. Ecomorphs (sensu Copilaș-Ciocianu & Sidorov, 2022) are indicated with labels.
FIGURE 2 in New Miocene fossil taxa illuminate the evolution and paleobiogeography of the Ponto-Caspian gammaroid amphipod radiation
FIGURE 2 Phylogenetic relationships among Ponto-Caspian gammaroids based on 114 morphological characters. Non-monotypic genera are highlighted in color. The fossil clade is highlighted with orange and a dagger symbol. Number at nodes represent support values for maximum likelihood (UFBS – ultrafast bootstrap, SHaLRT – Shimodaira-Hasegawa approximate likelihood ratio test), Bayesian (PP – posterior probability), and parsimony (JKBS – jackknifing bootstrap) analyses. Strongly supported nodes are highlighted with a green dot (UFBS ≥ 90; SHaLRT ≥ 80; PP ≥ 0.9; JKBS ≥ 90). Nodes that are not annotated received weak to no support (UFBS ≤ 50; SHaLRT ≤ 50; PP ≤ 0.5; JKBS ≤ 50).
FIGURE 1 Paleogeographic and geological setting. A in New Miocene fossil taxa illuminate the evolution and paleobiogeography of the Ponto-Caspian gammaroid amphipod radiation
FIGURE 1 Paleogeographic and geological setting. A) Map of the Ponto-Caspian region. The area marked with transparent white indicates the maximum extent of the Paratethys 11 Ma ago (Palcu et al., 2021). The green dot represents the newly discovered fossil amphipod sites from Romania, while the black dots indicate previously known fossiliferous locations from the Caucasus (Azerbaijan and Russia). B) Close-up map of Iași City, Romania, (https://www.openstreetmap.org /#map=12/47.1449/27.6062) showing the location of the study sites (Site 1 – construction site in Iași City; Site 2 – Vlădiceni quarry). C) Upper part shows a chronostratigraphic chart of the Eastern Paratethys and its correlation to the Global Time Scale (Raffi et al., 2020). The stratigraphic age of the sites from this study are indicated with green, while the previously known sites from the Caucasus are indicated with black. The lower part is a geological cross section of the focal area indicating the lithostratigraphic context and altitude (modified after Ionesi et al. 2005). Sampling sites are indicated with green dots. D) Photographs of the two study sites from the current study. PHOTO BY IONESI V.
FIGURE 7 in New Miocene fossil taxa illuminate the evolution and paleobiogeography of the Ponto-Caspian gammaroid amphipod radiation
FIGURE 7 †Eogmelina moldavica gen. et sp. nov. next to a fossilized alga (inventory No. 8240, Vlădiceni quarry). Scale bar = 5 mm.
Dataset from: Rapid radiation of ant parasitic butterflies during the Miocene aridification of Africa
<p>Africa has undergone a progressive aridification during the last 20 My that presumably impacted organisms and fostered the evolution of life history adaptations. We test the hypothesis that shift to living in ant nests and feeding on ant brood by larvae of phyto-predaceous <em>Lepidochrysops</em> butterflies was an adaptive response to the aridification of Africa that facilitated the subsequent radiation of butterflies in this genus. Using anchored hybrid enrichment we constructed a time-calibrated phylogeny for <em>Lepidochrysops</em> and its closest, non-parasitic relatives in the<em> Euchrysops </em>section (Poloyommatini). We estimated ancestral areas across the phylogeny with process-based biogeographical models and diversification rates relying on time-variable and clade-heterogeneous birth-death models.<strong> </strong>The <em>Euchrysops </em>section originated with the emerging Miombo woodlands about 22 million years ago (Mya), and spread to drier biomes as they became available in the late Miocene. The diversification of the non-parasitic lineages decreased as aridification intensified around 10 Mya, culminating in diversity decline. In contrast, the diversification of the phyto-predaceous <em>Lepidochrysops</em> lineage proceeded rapidly from about 6.5 Mya when this unusual life history likely first evolved.<strong> </strong>The Miombo woodlands were the cradle for diversification of the <em>Euchrysops</em> section, and our findings are consistent with the hypothesis that aridification during the Miocene selected for a phyto-predaceous life history in species of <em>Lepidochrysops</em>, with ant nests likely providing caterpillars a safe refuge from fire and a source of food when vegetation was scarce.</p>
Fig. 4 in A new ape from Türkiye and the radiation of late Miocene hominines
Fig. 4 Strict consensus cladograms. The four taxon sets each produced cladograms with the same topology whether character states were left unordered or a subset were ordered (see Methods and Supplementary Note 5 for details). a 18 OTUs. The four taxa with the fewest codable character states (Graecopithecus, 10%, Chororapithecus,13%, Samburupithecus, 18%, and Orrorin, 29%) were excluded, as was Sahelanthropus. Both Orrorin and Sahelanthropus were coded from published descriptions, which introduces uncertainty (DRB, who coded all characters in this analysis, was unable to code characters from these taxa through direct observation). b 19 OTUs, with Sahelanthropus added. c 20 OTUs with Orrorin. There is a decrease in resolution with the inclusion of Sahelanthropus and Orrorin but the tree topologies are otherwise consistent. Sahelantthropus is always recovered as a stem hominid and Orrorin as a hominin. The first three cladograms all recover a hominine clade that includes the thickly enameled Balkan taxa and the dryopithecins. d 23 OTUs, including all taxa. Little resolution remains among hominids, with recognized clades (pongines) unresolved. This cladogram also fails to recover Ouranopithecus as a hominine, which is otherwise a common result in previous analyses. Bremer support values, character states, character definitions and the character matrix (nexus) are all included in Supplementary Note 5 and Supplementary Data 3.
Fig. 3 3-D in A new ape from Türkiye and the radiation of late Miocene hominines
Fig. 3 3-D reconstruction of the left P3 to M1 of CO 300, showing the root, root canal and pulp chamber configurations. Supplementary Table 5 for a comparison of root formulae. Scale =10 mm.
Fig. 5 A in A new ape from Türkiye and the radiation of late Miocene hominines
Fig. 5 A phylogeny of the taxa included in this analysis consistent with most of the cladograms presented here. Taxa are positioned in chronological order without regard to geography, with most taxa only known from a limited time span. Exceptions are Ekembo and Sivapithecus, with longer time ranges, which are positioned roughly when they are most abundant, in both cases about mid-way in their known time ranges. The different colored "puddles" represent hominid clades and/or stages of evolution. These can also be imagined as pools of related species in somewhat delimited space and time with broad ancestordescendant relationships. The lines are disconnected to reflect the difficulty in identifying actual ancestor-descendant relationships, but that these relations can be estimated between "puddles". Blue puddle taxa are stem hominids and are all confined to Africa. Among these taxa the relations of Samburupithecus and Chororapithecus are unresolved in the cladograms except in so far as they are excluded from the clade that includes all Eurasian taxa and crown hominins. Other lines of evidence suggest that these taxa are members of the early or middle Miocene radiation of early apes (see text). The orange puddles are the pongines, which probably have their origin within the middle Miocene puddle, although not necessarily any of the taxa included here (another taxon, Griphopithecus, known from Europe and Türkiye, would be a member of the blue puddle but was not included in the cladistic analyses). While both are pongines, Ankarapithecus lacks derived features shared by Sivapithecus and Pongo, so the line representing the relationship between the latter two bi-passes Ankarapithecus. The three green-shade puddles represent the hominine clades as defined here. Bright green are the dryopithecins, with the younger taxa Rudapithecus and Hispanopithecus depicted as closely related and descendant from any of the older taxa or an unknown taxon sharing attributes with these three. The light green puddle includes the Balkan and Anatolian taxa, likely to have descended from somewhere in the dryopithecin puddle. Possible ancestor-descendant relationships are depicted in this puddle. The darker green puddle represents the crown hominines. The various lineages diverge from unknown ancestors, but probably a member of either of the older green shade puddles. Gorillas diverge first, followed by chimpanzees and humans. Orrorin and Ardipithecus are depicted in a manner consistent with their sister clade status, without implying a direct ancestor-descendant relationship.
Fig. 2 in A new ape from Türkiye and the radiation of late Miocene hominines
Fig. 2 Cross sectional anatomy of the palate in Anadoluvius and other hominids (not to scale). Ekembo and extant hominids redrawn from31 Rudapithecus modified from40. Ouranopithecus redrawn from41 based on a ct scan. The Ardipithecus specimen, modified from42, is a surface rendering derived from ct scans and does not show the cross section but the lateral aspect. The Ekembo specimen is based on BMNH 16664, the holotype of Ekembo nyanzae. The Rudapithecus specimens are RUD 12, a female, and RUD 44, a male. The photographs to the right of the line drawings of Rudapithecus are the original specimens. The Anadoluvius specimens are CO-2100/2800 (female, left) and CO-205 (male, right), with photographs of casts of the reconstructed specimens (see SI for details of the reconstruction.) Line drawings of Anadoluvius are original to this work.
Data from: Central Asian radiation of modern large-mammal faunas in mid-Miocene
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To mate, or not to mate: the evolution of reproductive diapause facilitates insect radiation into African savannahs in the Late Miocene
<p>1. Many tropical environments experience cyclical seasonal changes, frequently with pronounced wet and dry seasons, leading to a highly uneven temporal distribution of resources. Short-lived animals inhabiting such environments often show season-specific adaptations to cope with alternating selection pressures. 2. African Bicyclus butterflies show strong seasonal polyphenism in a suite of phenotypic and life-history traits, and their adults are thought to undergo reproductive diapause associated with the lack of available larval host plants during the dry season. 3. Using three years of longitudinal field data for three species in Malawi, dissections demonstrated that one forest species reproduces continuously whereas two savannah species undergo reproductive diapause in the dry season, either with or without pre-diapause mating. Using additional data from field-collected and museum samples, we then documented the same three mating strategies for a further 37 species. 4. Phylogenetic analyses indicated that the ancestral state was a non-diapausing forest species, and that habitat preference and mating strategy evolved in a correlated fashion. 5. Bicyclus butterflies underwent rapid diversification during the Late Miocene, coinciding with expansions into more open savannah habitat. We conclude that the ability to undergo reproductive diapause was a key trait that facilitated colonization and eventual radiation into savannahs in the Late Miocene.</p>
Data from: Miocene dispersal drives island radiations in the palm tribe Trachycarpeae (Arecaceae)
The study of three island groups of the palm tribe Trachycarpeae (Arecaceae/Palmae) permits both the analysis of each independent radiation and comparisons across the tribe to address general processes that drive island diversification. Phylogenetic relationships of Trachycarpeae were inferred from three plastid and three low-copy nuclear genes. The incongruent topological position of Brahea in CISP5 was hypothesized to be caused by duplication event and was addressed using uninode coding. The resulting phylogenetic trees were well-resolved and the genera were all highly-supported except for Johannesteijsmannia and Serenoa. Divergence time analysis estimated the stem of the tribe to be ca. 86 Ma ca. and the crown to be 38 Ma, indicating that significant extinction may have occurred along this branch. Historical biogeographic analysis suggested that Trachycarpeae are of southern North American, Central American, or Caribbean origin and supports previous hypotheses of a Laurasian origin. The biogeography and disjunctions within the tribe were interpreted with respect to divergence times, the fossil record, and geological factors such as the formation of the Greater Antilles - Aves Ridge, the Bering, and the North Atlantic land bridges, tectonic movement in Southeast Asia, climatic shifts between the Eocene and Pliocene, and volcanism in the Pacific basin. In considering the three major island radiations within Trachycarpeae, Miocene dispersal appears to have been the driving force in allopatric speciation and is highlighted here as an emerging pattern across the tree of life.
Importance of Longwave Radiative Forcing by Icy Clouds in Maintaining Miocene High-latitude Warmth
<p>Supporting Information for<strong> Importance of Longwave Radiative Forcing by Icy Clouds in Maintaining Miocene High-latitude Warmth</strong></p> <p>NetCDF files: B.MIO_400_C5.cam2.h0.last50yr_climo_monthly.nc is from our control experiment, and B.MIO_400_C5_MK_TeoKor_Dem1SLF_2.cam2.h0.last50yr_climo_monthly is from our modified experiment.</p> <p>cldwat2m_micro.F90, microp_aero.F90, microp_driver.F90, and zm_conv.F90 are the source code used in our modified experiment. </p> <p> </p>
Data from: A phylogenetic and morphologic context for the radiation of an endemic fauna in a long-lived lake: Corbulidae (Bivalvia; Myoida) in the Miocene Pebas Formation of western Amazonia
The Corbulidae are one of a handful of a primarily marine bivalve clades that exhibit a remarkable radiation, marked by increased species richness and divergent morphologies, within a long-lived lake. For corbulids, this diversification occurred within the lower to middle Miocene Pebas Formation of western Amazonia. Only one taxon associated with this radiation (Anticorbula) remains extant. We conducted a series of phylogenetic analyses to characterize diversification of Corbulidae within the Pebas Formation and relate that diversification to geologically older freshwater corbulids from the Paleocene Fort Union Formation of the northern Great Plains (United States). We used these results, as well as a quantitative examination of morphospace occupation, to infer whether Pebasian corbulids represent a true species flock, and whether the lacustrine system represented by the Pebas Formation represents a cradle of, or reservoir for, freshwater corbulid diversity. We conducted two sets of phylogenetic analyses using shell morphology characters. A genus-level data set incorporated type species of freshwater corbulid genera, any Paleocene representatives of these genera, and selected brackish and marine corbulid genera. A species-level analysis added all described freshwater corbulid taxa to the genus-level matrix. Our results were highly resolved (few most-parsimonious trees), but not particularly robust (low branch support). For the genus-level matrix, we used a taxon jackknife procedure to explore the effects of taxon sampling on tree stability and topology. Jackknife results recover a subclade of freshwater taxa (including both Anticorbula and Pachydon species and the Paleocene Ostomya sp.) in 92.4% of trees, although placement of this subclade across the ingroup varies, as do the topologic positions of other freshwater species. Freshwater and marine corbulids also are morphologically distinct from each other, a factor that likely reduced the robustness of our phylogenetic results. By combining these results with paleoecologic, stratigraphic, and morphologic data, we infer that freshwater corbulids arose once within the family, prior to the Cenozoic, with three distinct freshwater lineages present at their first appearance in the late Paleocene of North America. Within the Miocene Pebas system of South America, we reconstruct supralimital morphologic evolution within three lineages as freshwater taxa became variously adapted to the fluid, dysoxic muds characterizing lake-bottom facies representative of the Pebas lacustrine system. In addition, corbulids apparently successfully coped with high predation pressures from co-occurring shellcrushing predators. Finally, we consider that freshwater Corbulidae were primarily fluvial taxa throughout their geologic history, with a relatively ephemeral radiation within the Pebasian lake system, thus making the Pebasian system a cradle of diversity for several corbulid lineages.
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