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33 results for “Ancient History”
Ancient mitogenomes reveal the evolutionary history and biogeography of sloths
<p><strong>Supplementary Material for:</strong></p> <p>Delsuc F., Kuch M., Gibb G.C., Karpinski E., Hackenberger D., Szpak P., Martínez J.G., Mead J.I., McDonald H.G., MacPhee R.D.E., Billet G., Hautier L., and Poinar H.N. (2019). Ancient mitogenomes reveal the evolutionary history and biogeography of sloths. Current Biology. doi:10.1016/j.cub.2019.05.043.</p> <p> </p> <p><strong>Delsuc-CurrBiol-2019_capture_baits.fasta: </strong>Sequence baits designed from living xenarthran mitogenomes and reconstructed ancestral sequences used to capture ancient sloth mitogenomes. </p> <p><strong>Delsuc-CurrBiol-2019_dataset.fasta:</strong> Mitogenomic dataset used for phylogenetic reconstruction and molecular dating in fasta format.</p> <p><strong>Delsuc-CurrBiol-2019_dataset.phylip:</strong> Mitogenomic dataset used for phylogenetic reconstruction and molecular dating in phylip format.</p> <p><strong>Delsuc-CurrBiol-2019_dataset_partitions.nex:</strong> Mitogenomic dataset used for phylogenetic reconstruction and molecular dating in nexus format with partitions.</p> <p><strong>Delsuc-CurrBiol-2019_FigS2_RAxML_MLtree_100BP_nexus_for_FigTree.tree: </strong>Maximum likelihood mitogenomic tree inferred under the best-fitting partitioned model using RAxML. Related to Figure 1.<strong> </strong>Maximum-likelihood bootstrap percentages are indicating at nodes (100 replicates). Tree is rooted on midpoint. Scale is in mean number of substitutions per site. Tree in nexus format viewable with FigTree.</p> <p><strong>Delsuc-CurrBiol-2019_FigS3_IQ-TREE_MLtree_100BP_nexus_for_FigTree.tree</strong><strong>:</strong> Maximum likelihood mitogenomic tree inferred under the best-fitting partitioned model using IQ-TREE. Related to Figure 1. Maximum-likelihood bootstrap percentages are indicating at nodes (100 replicates). Tree is rooted on midpoint. Scale is in mean number of substitutions per site. Tree in nexus format viewable with FigTree.</p> <p><strong>Delsuc-CurrBiol-2019_FigS4_MrBayes_consensus_nexus_for_FigTree.tree: </strong>Bayesian consensus mitogenomic tree inferred under the best-fitting partitioned model using MrBayes. Related to Figure 1. Clade posterior probabilities (PP) are indicated at nodes. Tree is rooted on midpoint. Scale is in mean number of substitutions per site. Tree in nexus format viewable with FigTree. </p> <p><strong>Delsuc-CurrBiol-2019_FigS5_PhyloBayes_consensus_nexus_for_FigTree.tree: </strong>Bayesian consensus mitogenomic tree inferred under the CAT-GTR+G<sub>4</sub> mixture model using PhyloBayes. Related to Figure 1. Clade posterior probabilities (PP) are indicated at nodes. Tree is rooted on midpoint. Scale is in mean number of substitutions per site. Tree in nexus format viewable with FigTree.</p> <p><strong>Delsuc-CurrBiol-2019_FigS6_PhyloBayes_chronogram_nexus_for_FigTree.tree</strong><strong>: </strong>Bayesian mitogenomic chronogram. Related to Figure 2. This chronogram was inferred under the CAT-GTR+G<sub>4</sub> mixture model and an autocorrelated lognormal model of clock relaxation using PhyloBayes. Tree in nexus format viewable with FigTree.</p> <p><strong>Delsuc-CurrBiol-2019_Megatherium_bone_extraction_protocol.pdf: </strong>Detailed protocol for <em>Megatherium americanum</em> MAPB4R 3965 bone sample preparation.</p> <p><strong>Delsuc-CurrBiol-2019_ML_ancestral_reconstruction_MOL_constraint.pdf: </strong>Maximum likelihood ancestral character state reconstruction.<strong> </strong>Related to Figure 3. Maximum likelihood estimation of ancestral states for six dental characters from Varela et al. (2019) under the Mk model on the maximum likelihood topology obtained using the molecular topology as a backbone constraint. </p> <p><strong>Delsuc-CurrBiol-2019_ML_ancestral_reconstruction_MORPH_constraint.pdf: </strong>Maximum likelihood ancestral character state reconstruction.<strong> </strong>Related to Figure 3. Maximum likelihood estimation of ancestral states for six dental characters from Varela et al. (2019) under the Mk model on the maximum likelihood topology obtained using the same topological constraint that these authors used in their Bayesian phylogenetic reconstructions. </p> <p><strong>Delsuc-CurrBiol-2019_MP_ancestral_reconstruction_MOL_constraint.pdf: </strong>Maximum parsimony ancestral character state reconstruction.<strong> </strong>Related to Figure 3. Maximum parsimony estimation of ancestral states for six dental characters from Varela et al. obtained using the molecular topology as a backbone constraint.</p> <p><strong>Delsuc-CurrBiol-2019_MP_ancestral_reconstruction_MORPHO_constraint.pdf: </strong>Maximum parsimony ancestral character state reconstruction.<strong> </strong>Related to Figure 3. Maximum parsimony estimation of ancestral states for six dental characters from Varela et al. (2019) on the maximum parsimony topology obtained using the same topological constraint that these authors used in their Bayesian phylogenetic reconstructions. </p> <p><strong>Delsuc-CurrBiol-2019_TableS1_PartitionFinder_RAxML_best_partition_scheme.txt: </strong>Detailed results of the PartitionFinder analysis for RAxML.</p> <p><strong>Delsuc-CurrBiol-2019_TableS2_ModelFinder_IQ-TREE_best_partition_scheme.txt: </strong>Detailed results of the ModelFinder analysis for IQ-TREE.</p> <p><strong>Delsuc-CurrBiol-2019_TableS3_PartitionFinder_MrBayes_best_partition_scheme.txt: </strong>Detailed results of the PartitionFinder analysis for MrBayes.</p> <p> </p>
Evolutionary history of the Galápagos Rail revealed by ancient mitogenomes and modern samples
<p>Beast v. 2.6.3 input (<em>.xml</em>) files and output (<em>.log</em> and <em>.trees</em>) files for phylogenetic analyses of rails, used to determined the evolutionary history of the Galápagos Rail <em>Laterallus spilonota</em>. There are two main datasets: coding sequences of the mitochondrial genome ('mtCDS'), partitioned per codon position, and a two mitochondrial/one nuclear marker dataset ('2mt1nc'). For each of the datasets, separate runs have been made in which the fossil calibration of Rallidae is applied to the stem of the present-day family ('calRallidaeStem') or the crown node ('calRallidaeCrown), and finally all runs have been replicated with three different starting seeds ('seed_NNNNNNNNN', with the different seeds 123456789, 456789123, and 789123456).</p> <p>We provide raw output (<em>.log</em> and <em>.raw.trees</em>) as well as maximum clade credibility ('mcc') trees (<em>.mcc.trees</em>), calculated after discarding 10% of the trees as burn-in, using median ('heights_median') or mean ('heights_mean') node heights as estimated node age.</p> <p>The runs used for Table 1 (and Figure 2) in the accompanying paper are:</p> <ul> <li>Dataset mtCDS, Rallidae calibration of stem: seed 123456789</li> <li>Dataset mtCDS, Rallidae calibration of crown: seed 456789123 </li> <li>Dataset 2mt1nc, Rallidae calibration of stem: seed 789123456</li> <li>Dataset 2mt1nc, Rallidae calibration of crown: seed 123456789</li> </ul> <p>This version of the data includes <em>Pellornis mikkelseni</em> among the fossils making up the calibration distribution for crown Gruiformes. In a previous version of this data deposit, that data point was represented by <em>Messelornis cristata </em>(see accompanying paper).</p>
Our Mythical History: Children's and Young Adults' Culture in Response to the Heritage of Ancient Greece and Rome
<p>A short movie from the international conference <strong><em>Our Mythical History: Children’s and Young Adults’ Culture in Response to the Heritage of Ancient Greece and Rome </em></strong>held at the Faculty of "Artes Liberales", University of Warsaw, May 22-26, 2019</p> <p>available at <a href="https://www.youtube.com/watch?v=jVeEjWSCXD8">https://www.youtube.com/watch?v=jVeEjWSCXD8</a> </p> <p>Music: <em>Brave </em>by WildKitty Tunes, Video: Mirosław Kaźmierczak, Coordination: Katarzyna Marciniak</p> <p>Art works used in the movie: Matylda Tracewska, Zbigniew Karaszewski</p>
Figure 8 in The Iberian Peninsula: ancient history of a hot spot of mite harvestmen (Arachnida: Opiliones: Cyphophthalmi: Sironidae) diversity
Figure 8. Paramiopsalis eduardoi sp. nov., confocal laser scanning micrograph of the spermatopositor of a male paratype, dorsal view. Total length is 180 Mm.
Figure 5 in The Iberian Peninsula: ancient history of a hot spot of mite harvestmen (Arachnida: Opiliones: Cyphophthalmi: Sironidae) diversity
Figure 5. Paramiopsalis eduardoi sp. nov., scanning electron microgarphs of a male paratype. A, ventral view of whole body. B, ozophore. C, prosomal ventral complex. D, anal region. E, spiracle.
Figure 4 in The Iberian Peninsula: ancient history of a hot spot of mite harvestmen (Arachnida: Opiliones: Cyphophthalmi: Sironidae) diversity
Figure 4. Paramiopsalis eduardoi sp. nov., paratype female. A, dorsal view. B, ventral view. C, lateral view. Scale bars: 0.5 mm.
Figure 9 in The Iberian Peninsula: ancient history of a hot spot of mite harvestmen (Arachnida: Opiliones: Cyphophthalmi: Sironidae) diversity
Figure 9. Phylogeny of selected members of the family Sironidae, based on the combined analysis of 18S, 28S, cytochrome c oxidase subunit I (COI), and 16S under direct optimization and equal weighting. The support values on branches indicate the jackknife frequencies. Each weighting scheme is assigned a code corresponding to the ratio of indel/transversion, transversion/transition, and transition values. Tree lengths for the different parameter sets are as follows: 111, 2914; 121, 4585; 211, 3228; 3221, 6168. Black squares indicate monophyly; grey squares indicate that either the group is paraphyletic or the internal relationships are different.
Figure 7 in The Iberian Peninsula: ancient history of a hot spot of mite harvestmen (Arachnida: Opiliones: Cyphophthalmi: Sironidae) diversity
Figure 7. Paramiopsalis eduardoi sp. nov., scanning electron microgarphs of the legs of a male paratype. A, metatarsus and tarsus I. B, tarsal claw I. C, metatarsus and tarsus II. D, tarsal claw II. E, metatarsus and tarsus III. F, tarsal claw III. G, metatarsus and tarsus IV. H, detail of the adenostyle. I, tarsal claw IV.
Figure 2. Parasiro coiffaiti Juberthie, 1956, lectotype male. A, dorsal view. B, ventral view. C in The Iberian Peninsula: ancient history of a hot spot of mite harvestmen (Arachnida: Opiliones: Cyphophthalmi: Sironidae) diversity
Figure 2. Parasiro coiffaiti Juberthie, 1956, lectotype male. A, dorsal view. B, ventral view. C, lateral view. Scale bars: 0.5 mm.
Disentangling complex histories of hybridisation: The genomic consequences of ancient and recent introgression in Channel Island monkeyflowers
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Data from: The history of tree and shrub taxa on Bol'shoy Lyakhovsky Island (New Siberian Archipelago) since the last interglacial uncovered by sedimentary ancient DNA and pollen data
<p>Ecosystem boundaries, such as the Arctic-Boreal treeline, are strongly coupled with climate and were spatially highly dynamic during past glacial-interglacial cycles. Only a few studies cover vegetation changes since the last interglacial, as most of the former landscapes are inundated and difficult to access. Using pollen analysis and sedimentary ancient DNA (<span class="html-italic">s</span>edaDNA) metabarcoding, we reveal vegetation changes on Bol'shoy Lyakhovsky Island since the last interglacial from permafrost sediments. Last interglacial samples depict high levels of floral diversity with the presence of trees (<em><span class="html-italic">Larix</span></em>,<span class="html-italic"> <em>Picea</em></span>,<span class="html-italic"> <em>Populus</em></span>) and shrubs (<em><span class="html-italic">Alnus</span></em>, <em><span class="html-italic">Betula</span></em>, <em><span class="html-italic">Ribes</span></em>, <span class="html-italic"><em>Cornus</em>, </span>Saliceae) on the currently treeless island. After the Last Glacial Maximum, <em><span class="html-italic">Larix</span> </em>re-colonised the island but disappeared along with most shrub taxa. This was probably caused by Holocene sea-level rise, which led to increased oceanic conditions on the island. Additionally, we applied two newly developed larch-specific chloroplast markers to evaluate their potential for tracking past population dynamics from environmental samples. The novel markers were successfully re-sequenced and exhibited two variants of each marker in last interglacial samples. SedaDNA can track vegetation changes as well as genetic changes across geographic space through time and can improve our understanding of past processes that shape modern patterns.</p>
Fast diversification through a mosaic of evolutionary histories characterizes the endemic flora of ancient Neotropical mountains
<p><span><span><span><span><span><span><span><span><span><span><span>Mountains are among the most biodiverse areas on the globe. In young mountain ranges, exceptional plant species-richness is often associated to recent and rapid radiations linked to the mountain uplift itself. In ancient mountains, however, orogeny vastly precedes the evolution of vascular plants, so species-richness has been explained by species accumulation during long periods of low extinction rates. Here we evaluate these assumptions by analyzing plant diversification dynamicsin the<i>campo rupestre</i>, an ecosystem associated to pre-Cambrian mountaintops and highlands of eastern South America, areas where plant species-richness and endemism are among the highest in the world. Analyses of 15 angiosperm clades show that radiations of endemics present fastest rates of diversification during the climatically unstable period of the last 5 million years. However, results from ancestral range estimations using different models disagree on the age of the earliest <i>in situ</i>speciation events and point to a complex floristic assembly. There is a general trend for higher diversification rates associated to these areas, but endemism may also increase or reduce extinction rates, depending on the group. Montane habitats, no matter their geological age, may lead to boosts in speciation rates by accelerating population isolation in archipelago-like systems, circumstances that can also result in higher extinction rates and fast species turnover, misleading age estimates of endemic lineages. </span></span></span></span></span></span></span></span></span></span></span></p>
Ancient mitochondrial genomes unveil the origins and evolutionary history of New Zealand's enigmatic takahe and moho
<p>Many avian species endemic to Aotearoa New Zealand were driven to extinction or reduced to relict populations following successive waves of human arrival, due to hunting, habitat destruction, and the introduction of mammalian predators. Among the affected species were the large flightless South Island takahe (<em>Porphyrio hochstetteri</em>) and the moho (North Island takahe; <em>P. mantelli</em>), with the latter rendered extinct and the former reduced to a single relictual population. Little is known about the evolutionary history of these species prior to their decline and/or extinction. Here we sequenced mitochondrial genomes from takahe and moho subfossils (12 takahe and four moho) and retrieved comparable sequence data from takahemuseum skins (n = 5) and contemporary individuals (n = 17) to examine the phylogeny and recent evolutionary history of these species. Our analyses suggest that prehistoric takahepopulations lacked deep phylogeographic structure, in contrast to moho, which exhibited significant spatial genetic structure, albeit based on limited sample sizes (n = 4). Temporal genetic comparisons show that takahe have lost much of their mitochondrial genetic diversity, likely due to a sudden demographic decline soon after human arrival (~750 years ago). Time-calibrated phylogenetic analyses strongly support a sister-species relationship between takahe and moho, suggesting these flightless taxa diverged around 1.5 million years ago, following a single colonisation of New Zealand by a flighted <em>Porphyrio </em>ancestor approximately four million year ago. This study highlights the utility of palaeogenetic approaches for informing the conservation and systematic understanding of endangered species whose ranges have been severely restricted by anthropogenic impacts.</p>
Genetic admixture and evolutionary history of Han Chinese in the Shandong Peninsula inferred from integrative modern and ancient genomic resources
<p>The allele frequency data of 264 individuals from Shandong Province and supplementary table.</p>
Data from: The history of tree and shrub taxa on Bol'shoy Lyakhovsky Island (New Siberian Archipelago) since the last interglacial uncovered by sedimentary ancient DNA and pollen data
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Data from: The evolutionary history of the ancient weevil family Belidae (Coleoptera: Curculionoidea) reveals the marks of Gondwana breakup and major floristic turnovers, including the rise of angiosperms
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Ancient mitochondrial genomes unveil the origins and evolutionary history of New Zealand’s enigmatic takahe and moho
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Fast diversification through a mosaic of evolutionary histories characterizes the endemic flora of ancient Neotropical mountains
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Data from: Ancient mitochondrial genomes clarify the evolutionary history of New Zealand's enigmatic acanthisittid wrens
The New Zealand acanthisittid wrens are the sister-taxon to all other "perching birds" (Passeriformes) and – including recently extinct species – represent the most diverse endemic passerine family in New Zealand. Consequently, they are important for understanding both the early evolution of Passeriformes and the New Zealand biota. However, five of the seven species have become extinct since the arrival of humans in New Zealand, complicating evolutionary analyses. The results of morphological analyses have been largely equivocal, and no comprehensive genetic analysis of Acanthisittidae has been undertaken. We present novel mitochondrial genome sequences from four acanthisittid species (three extinct, one extant), allowing us to resolve the phylogeny and revise the taxonomy of acanthisittids. Reanalysis of morphological data in light of our genetic results confirms a close relationship between the extant rifleman (Acanthisitta chloris) and an extinct Miocene wren (Kuiornis indicator), making Kuiornis a useful calibration point for molecular dating of passerines. Our molecular dating analyses reveal that the stout-legged wrens (Pachyplichas) diverged relatively recently from a more gracile (Xenicus-like) ancestor. Further, our results suggest a possible Early Oligocene origin of the basal Lyall's wren (Traversia) lineage, which would imply that Acanthisittidae survived the Oligocene marine inundation of New Zealand and therefore that the inundation was not complete.
Data from: Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange, and distinct demographic histories
Widely distributed taxa provide an opportunity to compare biogeographic responses to climatic fluctuations on multiple continents and to investigate speciation. We conducted the most geographically and genomically comprehensive study to date of the red fox (Vulpes vulpes), the world's most widely distributed wild terrestrial carnivore. Analyses of 697 bp of mitochondrial sequence in ~1000 individuals suggested an ancient Middle Eastern origin for all extant red foxes and a 400 kya (SD = 139 kya) origin of the primary North American (Nearctic) clade. Demographic analyses indicated a major expansion in Eurasia during the last glaciation (~50 kya), coinciding with a previously described secondary transfer of a single matriline (Holarctic) to North America. In contrast, North American matrilines (including the transferred portion of Holarctic clade) exhibited no signatures of expansion until the end of the Pleistocene (~12 kya). Analyses of 11 autosomal loci from a subset of foxes supported the colonization timeframe suggested by mtDNA (and the fossil record) but, in contrast, reflected no detectable secondary transfer, resulting in the most fundamental genomic division of red foxes at the Bering Strait. Endemic continental Y-chromosome clades further supported this pattern. Thus, intercontinental genomic exchange was overall very limited, consistent with long-term reproductive isolation since the initial colonization of North America. Based on continental divergence times in other carnivoran species pairs, our findings support a model of peripatric speciation and are consistent with the previous classification of the North American red fox as a distinct species, V. fulva.
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