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389 results for “ancestral”
Data from: Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two ancestral sexual species
Quantifying introgression between sexual species and polyploid lineages traditionally thought to be asexual is an important step in understanding what drives the longevity of putatively asexual groups. Here, we capitalize on three recent innovations—ultraconserved element (UCE) sequencing, bioinformatic techniques for identifying genome-specific variation in polyploids, and model-based methods for evaluating historical gene flow—to measure the extent and tempo of introgression over the evolutionary history of an allopolyploid lineage of all-female salamanders and two ancestral sexual species. Our analyses support a scenario in which the genomes sampled in unisexual salamanders last shared a common ancestor with genomes in their parental species ~3.4 million years ago, followed by a period of divergence between homologous genomes. Recently, secondary introgression has occurred at different times with each sexual species during the last 500,000 years. Sustained introgression of sexual genomes into the unisexual lineage is the defining characteristic of their reproductive mode, but this study provides the first evidence that unisexual genomes have undergone long periods of divergence without introgression. Unlike other sperm-dependent taxa in which introgression is rare, the alternating periods of divergence and introgression between unisexual salamanders and their sexual relatives could explain why these salamanders are among the oldest described unisexual animals.
Bayesian inference of ancestral host-parasite interactions under a phylogenetic model of host repertoire evolution
<p>Intimate ecological interactions, such as those between parasites and their hosts, may persist over long time spans, coupling the evolutionary histories of the lineages involved. Most methods that reconstruct the coevolutionary history of such interactions make the simplifying assumption that parasites have a single host. Many methods also focus on congruence between host and parasite phylogenies, using cospeciation as the null model. However, there is an increasing body of evidence suggesting that the host ranges of parasites are more complex: that host ranges often include more than one host and evolve via gains and losses of hosts rather than through cospeciation alone. Here, we develop a Bayesian approach for inferring coevolutionary history based on a model accommodating these complexities. Specifically, a parasite is assumed to have a host repertoire, which includes both potential hosts and one or more actual hosts. Over time, potential hosts can be added or lost, and potential hosts can develop into actual hosts or vice versa. Thus, host colonization is modeled as a two-step process that may potentially be influenced by host relatedness. We first explore the statistical behavior of our model by simulating evolution of host-parasite interactions under a range of parameter values. We then use our approach, implemented in the program RevBayes, to infer the coevolutionary history between 34 Nymphalini butterfly species and 25 angiosperm families. Our analysis suggests that host relatedness among angiosperm families influences how easily Nymphalini lineages gain new hosts.</p>
Ancestral reconstruction of sunflower karyotypes reveals non-random chromosomal evolution
<p>Mapping the chromosomal rearrangements between species can inform our understanding of genome evolution, reproductive isolation, and speciation. Here we present a novel algorithm for identifying regions of synteny in pairs of genetic maps, which is implemented in the accompanying R package, syntR. The syntR algorithm performs as well as previous methods while being systematic and repeatable and can be used to map chromosomal rearrangements in any group of species. In addition, we present a systematic survey of chromosomal rearrangements in the annual sunflowers, which is a group known for extreme karyotypic diversity. We build high-density genetic maps for two subspecies of the prairie sunflower<i>,</i> <i>Helianthus</i> <i>petiolaris</i> ssp. <i>petiolaris</i> and <i>H. petiolaris</i> ssp. <i>fallax.</i> Using <i>syntR</i>, and we identify blocks of synteny between these two subspecies and previously published high-density genetic maps. We reconstruct ancestral karyotypes for annual sunflowers using those synteny blocks and conservatively estimate that there have been 7.9 chromosomal rearrangements per million years – a high rate of chromosomal evolution. Although the rate of inversion is even higher than the rate of translocation in this group, we further find that every extant karyotype is distinguished by between 1 and 3 translocations involving only 8 of the 17 chromosomes. This non-random exchange suggests that specific chromosomes are prone to translocation and may thus contribute disproportionately to widespread hybrid sterility in sunflowers. These data deepen our understanding of chromosome evolution and confirm that <i>Helianthus</i> has an exceptional rate of chromosomal rearrangement that may facilitate similarly rapid diversification.</p>
Indigenous struggles to preserve the Atitlan Lake"Grandmother", ancestral territories and cultures, in San Pedro La Laguna, Sololá, Guatemala
<p>Presentation made at Panel 5, the Educational, Ethical, and Preservationist Water Question, The Youth and the Climatic Struggle, First International Forum of the Federal University of Pernambuco (UFPE), in Preparation for the 2025 UNCOP30, 21-24 November 2023 Recife, Pernambuco, Brazil.</p>
Dataset for the ancestral sequence reconstruction of NRC3
<p>Please refer to the material_and_method.pdf to check how we generated each file.</p><p> </p><p><strong>01_NRCH_cds_23-03-03.fasta</strong></p><p>FASTA file containing the nucleotide sequences of 2341 NRC helper sequences extracted from 124 Solanaceae NLRome dataset [1] and 20 NRC helper sequences from Adachi et al. 2023 [2].</p><p><br><strong>02_NRCH_cds_23-03-03.min2400max2800.fasta</strong></p><p>FASTA file containing the nucleotide sequences of 1753 NRC helper sequences filtered to keep only sequences between 2400 and 2800 bp.</p><p><br><strong>03_NRCH_cds_23-03-03.min2400max2800.uniq.fasta</strong></p><p>FASTA file containing the nucleotide sequences of 1116 NRC helper sequences filtered to keep only sequences between 2400 and 2800 bp and to remove duplicates.</p><p><br><strong>04_NRCH_cds_23-03-03.min2400max2800.uniq.NBARC_aa.fasta</strong></p><p>FASTA file containing the amino acid sequences of 1116 NB-ARC domains of NRC helpers after filtering to keep only sequences between 2400 and 2800 bp and to remove duplicates.</p><p><br><strong>05_NRCH_cds_23-03-03.min2400max2800.uniq.NBARC_aa.aln.fasta</strong></p><p>FASTA file containing the amino acid sequences of 1116 NB-ARC domains of NRC helpers after filtering to keep only sequences between 2400 and 2800 bp and to remove duplicates and after alignment with MAFFT.</p><p><br><strong>06_NRCH_cds_23-03-03.min2400max2800.uniq.NBARC_aa.aln.fasta.treefile</strong></p><p>Newick file containing the phylogenetic tree of the 1116 NB-ARC domains of NRC helpers reconstructed with FastTree.</p><p><br><strong>07_NRC123X_cds_23-03-03.min2400max2800.uniq.aa.fasta</strong></p><p>FASTA file containing the 324 full-length amino acid sequences of the NRC1/2/3/X clades.</p><p><br><strong>08_NRC123X_cds_23-03-03.min2400max2800.uniq.aa.aln.fasta</strong></p><p>FASTA file containing the 324 full-length amino acid sequences of the NRC1/2/3/X clades after alignment with MAFFT.</p><p><br><strong>09_NRC123X_cds_23-03-03.min2400max2800.uniq.nt.aln.fasta</strong></p><p>FASTA file containing the 324 full-length nucleotide sequences of the NRC1/2/3/X clades threaded onto the protein alignment with MAFFT.</p><p><br><strong>10_NRC123X_cds_23-03-03.min2400max2800.uniq.nt.aln.fasta.treefile</strong></p><p>Newick file containing the phylogenetic tree of the 324 full-length nucleotide sequences of the NRC1/2/3/X clades reconstructed with IQ-TREE.</p><p> </p><p><strong>11_FastML_NRC123X.zip</strong></p><p>Zip file containing the FastML results for the ancestral sequence reconstruction of the NRC1/2/3/X clades.</p><p> </p><p>1. Sugihara, Y., Toghani, A., Kamoun, S., & Kourelis, J. (2023). NLRome dataset from 124 genomes of plants in the Solanaceae family. <i>Zenodo</i>. https://doi.org/10.5281/zenodo.10354350</p><p>2. Adachi, H., Sakai, T., Harant, A., Pai, H., Honda, K., Toghani, A., Claeys, J., Duggan, C., Bozkurt, T. O., Wu, C., & Kamoun, S. (2023). An atypical NLR protein modulates the NRC immune receptor network in Nicotiana benthamiana. <i>PLOS Genetics</i>, 19(1), e1010500. https://doi.org/10.1371/journal.pgen.1010500</p><p> </p>
Ancestral Puebloan Clay Bowl High Res
Ancestral Puebloan clay bowl on display at the Hutchings Museum. 173 images, Canon EOS 80D, 35mm, F/16, ISO 100, Agisoft Metashape, Windows 10. Source: Objaverse 1.0 / Sketchfab
Ancestral allele estimates for cattle using est-sfs software with the K2 model
<h1>Overview</h1> <p>The assignment of bovine ancestral alleles was based on a model comparison of alleles from cattle with alleles from outgroup species: Water Buffalo, Sheep, and White-Tailed Deer. </p> <p>The frequency of cattle alleles are determined using 79 representative individuals from 1000 Bull Genomics Project. We utilized multiple sequence alignments of 110 species (78 ruminants and 32 mammalian outgroup species), available from http://animal.omics.pro/code/index.php/RGD/loadByGet?address[]=RGD/Download/comSynDownload.php, to determine the alleles in Water Buffalo, Sheep, and White-Tailed Deer at each locus.</p> <p>We employed the est-sfs software with the K2 model to infer the probability (Pancs) of the major allele in cattle being ancestral. Alleles were determined to be ancestral if they were the major allele at a site with Pancs > 0.8 or the minor allele at a site with Pancs < 0.2.</p> <p>Please email bft990914@163.com for any queries.</p> <p>The columns of this dataframe are</p> <p>chrome: chromosome index.</p> <p>pos: physical location of SNV.</p> <p>cattle_ref: reference allele of cattle.</p> <p>cattle_alt: alternative allele of cattle.</p> <p>cattle_maj: major allele of cattle.</p> <p>water_buffalo: the sequence of water_buffalo.</p> <p>sheep: the sequence of sheep.</p> <p>white_tailed_deer: the sequence of white_tailed_deer.</p> <p>p_maj_anc: the probability of the major allele of cattle being ancestral.</p> <p>ancestral_allele: the inferred ancestral allele.</p>
Dataset for "Ancient whale rhodopsin reconstructs dim-light vision over a major evolutionary transition: Implications for ancestral diving behaviour"
<p>Dataset files include:</p> <p>- Alignment of rhodopsin (Rh1) sequences formatted for PAML</p> <p>- Corresponding species tree in Newick format for PAML</p> <p>- Ancestral Rh1 amino acid sequences (for Cetacean and Whippomorpha nodes) estimated with PAML (random sites, clade, and amino acid models), Datamonkey, and ProtASR</p>
A dynamic ancestral graph model and GPU-based simulation of a community based on metagenomic sampling
<p>In this paper we present an ancestral graph model of the evolution of a guild in an ecological community. The model is based on a metagenomic sampling design in that a random sample is taken at the community, as opposed the taxon, level and species are discovered by genetic sequencing. The specific implementation of the model envisions an ecological guild that was founded by colonization at some point in the past that then potentially undergoes diversification by natural selection. Within the graph, species emerge and evolve through the diversification process and their densities in the graph are dynamic and governed by both ecological drift and random genetic drift, as well as differential viability. We employ the 3% sequence divergence rule at a marker locus to identify Operational Taxonomic Units. We then explore approaches to see if there are indirect signals of the diversification process, including population genetic and ecological approaches. In terms of population genetics, we study the joint site frequency spectrum of OTUs, as well its associated statistics. In terms of ecology, we study the species (or OTU) abundance distribution. For both we observe deviations from neutrality, which indicates that there may be signals of diversifying selection in metagenomic studies under certain conditions. The model is available as a GPU-based computer program in C/C++ and using OpenCL, with the long-term goal of adding functionality iteratively to model large-scale eco-evolutionary processes for metagenomic data.</p>
Data From: Exploitation of an ancestral pheromone biosynthetic pathway contributes to diversification in Heliconius butterflies
<p class="MsoNormal"><span>During courtship, male butterflies produce androconial secretions containing male sex pheromones (MSPs) that communicate species identity and affect female choice. MSPs are thus likely candidates as reproductive barriers, yet their role in speciation remains poorly studied. Although <em>Heliconius </em>butterflies are a model system in speciation, their MSPs have not been investigated from a macroevolutionary perspective. We use GC-MS to characterise male androconial secretions in 33 of the 69 species in the Heliconiini tribe. We found these blends to be species-specific, consistent with a role in reproductive isolation. We detected a burst in blend diversification rate at the most speciose genus,<em> Heliconius</em>; a consequence of <em>Heliconius</em> and <em>Eueides</em> species using a fatty acid metabolic pathway to unlock more complex blends than basal Heliconiini species, whose secretions are dominated by plant derivatives. A comparison of 10 sister species pairs demonstrates a striking positive correlation between blend dissimilarity and range overlap, consistent with a scenario of character displacement or reinforcement in sympatry. These results demonstrate for the first time that MSP diversification can promote reproductive isolation across this group of butterflies, showcasing how re-activation of an ancestral trait, the co-option of the fatty acid metabolic pathway for pheromone production, can facilitate rapid speciation. </span></p>
Ancestral environment determines the current reaction to ultraviolet radiation in Daphnia magna
<p><span>An individual's phenotype can be altered by direct contact with its present environment but also by environmental features experienced by previous generations, i.e. parental or grandparental effects. However, the strength and direction of these transgenerational effects may be highly variable according to the ecological conditions experienced by ancestral generations. Here we performed a reciprocal split-brood experiment to compare transgenerational responses to the threat of ultraviolet radiation (UVR) in the zooplankter <em>Daphnia magna</em>, which had, or had not, been exposed to UVR for more than 150 generations, respectively. We found that the environment at which parents and grandparents were reared significantly influenced both behavior and life-history traits of their descendants. However, such transgenerational responses </span><span>differed between <em>D. magna</em> individuals with contrasting ancestral stress history</span><span>, that is, when exposed to UVR previously unexposed individuals rapidly changed their behavior and life-history traits, whereas individuals previously exposed to UVR showed less pronounced response when the UVR threat level relaxed. Hence, we here demonstrate an asymmetric transgenerational plasticity in response to UVR threat. The findings advance our understanding on the evolutionary ecology of such transgenerational effects and their potential role in response to changes in the local environment.</span></p>
ARPIP: Ancestral sequence Reconstruction with insertions and deletions under the Poisson Indel Process
<p>Modern phylogenetic methods allow inference of ancestral molecular sequences given an alignment and phylogeny relating present day sequences. This provides insight into the evolutionary history of molecules, helping to understand gene function and to study biological processes such as adaptation and convergent evolution across a variety of applications. Here we propose a dynamic programming algorithm for fast joint likelihood-based reconstruction of ancestral sequences under the Poisson Indel Process (PIP). Unlike previous approaches, our method, named ARPIP, enables the reconstruction with insertions and deletions based on an explicit indel model. Consequently, inferred indel events have an explicit biological interpretation. Likelihood computation is achieved in linear time with respect to the number of sequences. Our method consists of two steps, namely finding the most probable indel points and reconstructing ancestral sequences. First, we find the most likely indel points and prune the phylogeny to reflect the insertion and deletion events per site. Second, we infer the ancestral states on the pruned subtree in a manner similar to FastML. We applied ARPIP on simulated datasets and on real data from the Betacoronavirus genus. ARPIP reconstructs both the indel events and substitutions with a high degree of accuracy. Our method fares well when compared to established state-of-the-art methods such as FastML and PAML. Moreover, the method can be extended to explore both optimal and suboptimal reconstructions, include rate heterogeneity through time and more. We believe it will expand the range of novel applications of ancestral sequence reconstruction.</p>
Phylogenomics shows unique traits in Noctilucales are derived rather than ancestral
<p><span>Dinoflagellates are a diverse group of protists that possess many unique traits. These include (but are not limited to) expansive genomes packaged into permanently condensed chromosomes, photosynthetic or cryptic plastids acquired vertically or horizontally in serial endosymbioses, and a ruffle-like transverse flagellum attached along its length to the cell. When reconstructing </span><span>character evolution, early branching lineages with unusual features that distinguish them from the rest of the group have proven useful for inferring ancestral states. The Noctilucales are one such lineage, possessing relaxed chromosomes in some life stages and a trailing, thread-like transverse flagellum. However, most of the cellular and molecular data for the entire group come from a single cultured species, </span><em><span>Noctiluca scintillans</span></em><span>, and because its phylogenetic position is unresolved, it remains unclear if these traits are ancestral or derived. Here, we use single cell transcriptomics to characterize three diverse</span><span> Noctilucales genera: </span><em><span>Spatulodinium</span></em><span>, <em>Kofoidinium</em>, and a new lineage, <em>Fabadinium</em> gen. nov. We also provide transcriptomes for undescribed species in <em>Amphidinium</em></span><span> and Abediniales</span><span>, critical taxa for clarifying the phylogenetic position of </span><span>Noctilucales</span><span>. Phylogenomic analyses suggest that the Noctilucales are sister to <em>Amphidinium</em> rather than an independent branch outside the core dinoflagellates. This topology is consistent with observations of shared characteristics between some members of Noctilucales and <em>Amphidinium</em> and provides the most compelling evidence to date that the unusual traits within this group are derived rather than ancestral. We also confirm that <em>Spatulodinium</em> </span><span>plastids are photosynthetic and of ancestral origin</span><span>, and show that all non-photosynthetic Noctilucales retain plastid </span><span>genes</span><span> indicating a cryptic organelle.</span></p>
Ancestral Hopi Duck Effigy (Replica)
This model represents technology in my work coming full circle. This was my first try at replicating ancient Southwesern ceramics. I made this vessel with clay from the Homol'ovi region, based upon a design published from the excavation of Awat'ovi, in 1988. For giggles, I used reality capture to model the object, and today I went on to print the vessel in PLA. Good fun on a Saturday afternoon. Source: Objaverse 1.0 / Sketchfab
Ancestral Pueblo Pottery Sherd
This is a model of a pottery sherd from the Ancestral Pueblo. It was donated to the Rollins Teaching Collection with a number of other unprovenienced sherds. Model made by Bailey Allebach. Source: Objaverse 1.0 / Sketchfab
Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life
<p>For each ancestral gene, we assign a stable identifier, and provide additional information designed to facilitate analysis: an inferred name (based on its descendants in extant genomes), a reconstructed protein sequence, a set of inferred Gene Ontology (GO) annotations, and a “proxy gene” for each ancestral gene, defined as the least-diverged descendant of the ancestral gene in a given extant genome.</p>
Drumming in the Breaks of Olodum's Samba-Reggae: Ancestrality and Black Resistance in Salvador, Brazil
<p>I presented this video at the Southeast and Caribbean Ethnomusicology Chapter conference at the University of South Florida in Tampa, Florida, on March 2nd, 2024. </p>
Data from: Resegmentation is an ancestral feature of the gnathostome vertebral skeleton
<p>The vertebral skeleton is a defining feature of vertebrate animals. However, the mode of vertebral segmentation varies considerably between major lineages. In tetrapods, adjacent somite halves recombine to form a single vertebra through the process of 'resegmentation'. In teleost fishes, there is considerable mixing between cells of the anterior and posterior somite halves, without clear resegmentation. To determine whether resegmentation is a tetrapod novelty, or an ancestral feature of jawed vertebrates, we tested the relationship between somites and vertebrae in a cartilaginous fish, the skate (Leucoraja erinacea). Using cell lineage tracing, we show that skate trunk vertebrae arise through tetrapod-like resegmentation, with anterior and posterior halves of each vertebra deriving from adjacent somites. We further show that tail vertebrae also arise through resegmentation, though with a duplication of the number of vertebrae per body segment. These findings resolve axial resegmentation as an ancestral feature of the jawed vertebrate body plan.</p>
Ancestral sperm ecotypes reveal multiple invasions of a non-native fish in northern Europe
For externally fertilising organisms in the aquatic environment, the abiotic fertilisation medium can be a strong selecting force. Among bony fishes, sperm are adapted to function in a narrow salinity range. A notable exception is the family Gobiidae, where several species reproduce across a wide salinity range. The family also contains several wide-spread invasive species. To better understand how these fishes tolerate such varying conditions, we measured sperm performance in relation to salinity from a freshwater and a brackish population within their ancestral Ponto-Caspian region of the round goby, Neogobius melanostomus. These two ancestral populations were then compared to nine additional invaded sites across northern Europe, both in terms of their sperm traits and by using genomic SNP markers. Our results show clear patterns of ancestral adaptations to freshwater and brackish salinities in their sperm performance. Population genomic analyses show that the ancestral ecotypes have generally established themselves in environments that fit their sperm adaptations. Sites close to ports with intense shipping show that both outbreeding and admixture can affect the sperm performance of a population in a given salinity. Rapid adaptation to local conditions is also supported at some sites. Historical and contemporary evolution in the traits of the round goby sperm cells is tightly linked to the population and seascape genomics as well as biogeographic processes in these invasive fishes. Since the risk of a population establishing in an area is related to the genotype by environment match, port connectivity and the ancestry of the round goby population can likely be useful for predicting the species spread.
Conserved ancestral tropical niche but different continental histories explain the latitudinal diversity gradient in brush-footed butterflies
<p><strong>Supplementary Tree 1.nex</strong> Nymphalidae backbone tree inferred with RAxML and time-calibrated using BEAST, with mean posterior node ages and 95% credibility intervals summarized.</p> <p>More information can be found in Chazot <em>et al.</em> (2021). Conserved ancestral tropical niche but different continental histories explain the latitudinal diversity gradient in brush-footed butterflies. <em>Nature Communications.</em></p> <p> </p> <p><strong>Supplementary Tree 2</strong>.nex Maximum clade credibility tree of all Nymphalidae included in "Chazot <em>et al.</em> (2021). Conserved ancestral tropical niche but different continental histories explain the latitudinal diversity gradient in brush-footed butterflies. <em>Nature Communications."</em>, with mean posterior node ages and 95% credibility intervals estimated from the posterior distribution of 1000 grafted trees (1000 subclades posterior trees combined with 1000 backbone posterior trees). </p> <p>More information can be found in Chazot <em>et al.</em> (2021). Conserved ancestral tropical niche but different continental histories explain the latitudinal diversity gradient in brush-footed butterflies. <em>Nature Communications.</em></p>
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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