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389 results for “ancestral”

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dryad36/100

Data from: Ancestral area analyses reveal Pleistocene-influenced evolution in a clade of Coastal Plain endemic plants

AIM: The North American Coastal Plain is currently recognized as a global biodiversity hotspot. However, the mechanisms driving high levels of species richness in a region with relatively low topographic relief and homogeneous climate are unclear. We investigated the evolutionary processes driving ancestral area evolution and diversification in a biodiversity hotspot from both a systematic and biogeographic context using a clade endemic to the hotspot. LOCATION: North American Coastal Plain TAXON: The Scrub Mint clade comprises Dicerandra, Conradina, Piloblephis, Stachydeoma, and four species of Clinopodium (Mentheae; Lamiaceae), almost all of which are endemic to the North American Coastal Plain. METHODS: We generated a dated phylogeny using a target enrichment/capture dataset and then calculated ancestral area using biogeographic models. We uncovered neo- and paleo-endemism hotspots and inferred ancestral potential ranges at each node based on ancestral niche reconstructions and paleoclimatic data to understand the geographic range evolution of subclades. RESULTS: Ancestral area for the SMC was inferred to be the Florida Panhandle/Apalachicola River basin. A diversification event likely happened around the mid-Pleistocene Transition. Endemism hotspots were recovered in NE Florida, the Atlantic Coastal Ridge, and along the Lake Wales Ridge. Reconstructions of potential ranges support biogeographic findings, with the ancestor of the SMC likely located in the vicinity of the northeastern Gulf Coast during interglacial and glacial periods. MAIN CONCLUSIONS: The timing of diversification events and colonization of new areas by ancestors of the SMC is consistent with the timing of major geological events in the region. The presence of multiple types of endemism highlights the complexity of evolutionary and ecological processes that foster the large number of endemic taxa found in this region. Efforts to identify hotspots in this region will be critical to preserving the remaining pockets of biodiversity threatened by global change.

opencc-zeroOct 2022View details →

dryad36/100

Strong evidence for positive and negative correlational selection revealed by recreating ancestral variation

The study of adaptation helps explain biodiversity and predict future evolution. Yet the process of adaptation can be difficult to observe due to limited phenotypic variation in contemporary populations. Furthermore, the scarcity of male fitness estimates has made it difficult to both understand adaptation and evaluate sexual conflict hypotheses. We addressed both issues in our study of two anther position traits in wild radish (Raphanus raphanistrum): anther exsertion (long filament − corolla tube lengths) and anther separation (long − short filament lengths). These traits affect pollination efficiency and are particularly interesting due to the unusually high correlations among their component traits. We measured selection through male and female fitness on wild radish plants from populations artificially selected to recreate ancestral variation in each anther trait. We found little evidence for conflicts between male and female function. We found strong evidence for stabilizing selection on anther exsertion and disruptive selection on anther separation, indicating positive and negative correlational selection on the component traits. Intermediate levels of exsertion are likely an adaptation to best contact small bees. The function of anther separation is less clear, but future studies might investigate pollen placement on pollinators and compare species possessing multiple stamen types.

opencc-zeroNov 2022View details →

dryad36/100

Data from: The endocast of Euparkeria sheds light on the ancestral archosaur nervous system

Understanding the evolution of the tetrapod brain is essential to trace the history of ecomorphological diversification of modern clades. While previous studies focused on the morphological transformation of the nervous system along the dinosaur-bird transition, little is known about the brain anatomy of archosauriformes and early archosaurs. Here, we describe the endocast of Euparkeria capensis, a small-bodied, terrestrial archosauriform closely related to Archosauria, with the goal of resolving the current uncertainties surrounding the ancestral condition of the archosaurian nervous system. The endocast of Euparkeria is sigmoidal, with large olfactory bulbs, an expanded cerebral hemisphere and an elongated flocculus. We suggest that this pivotal taxon was an active predator with a remarkable olfactory acuity. Overall, the endocast of Euparkeria resembles the ones observed in phytosaurs, crocodilians and early dinosaurs, implying that modern crocodilians retain an archosaurian plesiomorphic brain morphology.

opencc-zeroNov 2022View details →

zenodo36/100

Supplemental Data File for Resetting Archaeological Interpretations of Pre-Contact Indigenous Agriculture: Maize Isotopic Evidence from Three Ancestral Mohawk Iroquoian Villages

Supplemental data tables for the paper "Resetting Archaeological Interpretations of Pre-Contact Indigenous Agriculture:  Maize Isotopic Evidence from Three Ancestral Mohawk Iroquoian Villages"  revised manuscript submitted for peer review.

opencc-by-4.0Feb 2023View details →

zenodo36/100

Data for Extremely sparse models of linkage disequilibrium in ancestrally diverse association studies

Data from Extremely sparse models of linkage disequilibrium in ancestrally diverse association studies (2023). This includes linkage disequilibrium graphical models (LDGMs) created from <a href="https://www.biorxiv.org/content/10.1101/2021.02.06.430068v2">high-coverage 1000 Genomes Project sequencing data</a>. This dataset consists of LDGM precision matrices, LDGM graphical models of SNPs, and lists of SNPs, all split into <a href="https://www.biorxiv.org/content/10.1101/2022.03.04.483057v1">1,361 approximately independent LD blocks across the genome</a>. The dataset additionally contains genotype information from chromosomes 21 and 22, and inferred tree sequences of high coverage 1000 Genomes Project Data, summary statistics from four traits in the UK Biobank, and UK biobank correlation matrices from chromosomes 21 and 22. All genomic data is in the GRCh38 build. The data can be cited as follows: Pouria Salehi Nowbandegani, Anthony Wilder Wohns, Jenna L. Ballard, Eric S. Lander, Alex Bloemendal, Benjamin M. Neale, and Luke J. O’Connor. Extremely sparse models of linkage disequilibrium in ancestrally diverse association studies. Nat Genet. (2023) DOI: 10.1038/s41588-023-01487-8   The directory contains `.tar.gz` files, which can be extracted and unzipped with: <pre><code class="language-bash">$ tar -xvf FILENAME.tar.gz</code></pre> All LD block files are named by chromosome and start/end basepair coordinates. <ul> <li> 1kg_nygc_trios_removed_All_pops_geno_ids_pops.csv: The file contains 5008 rows, 2 for each individual in the 1000 Genomes Project. Each row contains the individual ID of the 1000 genomes individual, and the ancestry group and continental ancestry group that individual was assigned to. Rows correspond to columns in `.genos` files.  </li> <li>AFR/AMR/EAS/EUR/SAS.precision.tar.gz: Precision matrices for the relevant ancestry group for each LD block. Edge lists contain one row for each non-zero entry of the precision matrix. There are no column names.</li> <li>genos_chr21_22.tar.gz: for the 40 LD blocks on chromosomes 21-22, .genos files are 0/1 matrices, with dimension number-of-SNPs by number-of-samples . Each LD matrix contains one column for each row in the SNP list files, and one row for each row in the sample ID files.</li> <li>ldgms.tar.gz: 1361 LDGMs (*.edgelist files). Edge lists contain one row for each non-zero entry of the LDGM adjacency matrix. There is one LDGM edge list for each LD block. Each row represents an edge, as a tuple (index_1, index_2, entry). For the LDGM adjacency matrices, the entry is the edge weight, where 0 represents a strong dependency and e.g. 6 represents a weak dependency.</li> <li>snplists_GRch38positions.tar.gz: 1361 *.snplist files, each of which contains information on the SNPs in each LD block. Each SNP list is an n x 11 table (n = number of SNPs), one for each LD block. The columns are:  <ul> <li> index: these non-unique indices, starting at zero, correspond to rows and columns of the LDGMs. There can be multiple SNPs for a single index, which occurs when the corresponding mutations occur on the same brick of the bricked tree sequence. SNPs with the same index have high (nearly perfect) LD. </li> <li> anc_alleles: ancestral allele </li> <li> deriv_alleles: derived allele </li> <li> EUR: allele frequency of derived allele in EUR samples </li> <li> EAS: allele frequency of derived allele in EAS samples </li> <li> AMR: allele frequency of derived allele in AMR samples </li> <li> SAS: allele frequency of derived allele in SAS samples </li> <li> AFR: allele frequency of derived allele in AFR samples </li> <li> site_ids: unique identifier of each SNP, mostly as RSIDs </li> <li> position: GRCh38 position of SNP </li> <li> swap: indicates strandness swap </li> </ul> </li> <li> ukb.tar: Correlation matrices and SNP lists for SNPs in the UK Biobank. <ul> <li> correlation_matrices/: Correlation matrices for SNPs in the UK biobank, computed by Weissbrod et al. 2020 Nat Genet and can be downloaded by following the instructions <a href="https://alkesgroup.broadinstitute.org/UKBB_LD">here</a>. </li> <li> snplists/: List of SNPs in the *.snplist format included in the UK Biobank </li> </ul> </li> <li> tree_seqs.tar: contains 22 tree sequences inferred by <a href="https://tsinfer.readthedocs.io">tsinfer</a> from the <a href="https://www.biorxiv.org/content/10.1101/2021.02.06.430068v2">30x 1000 Genomes Project Data</a>. Tree sequences can be unzipped with <a href="https://tszip.readthedocs.io/en/latest/">tszip</a>. </li> <li> Summary statistics: there are four summary statistics files, obtained from <a href="https://alkesgroup.broadinstitute.org/UKBB/">https://alkesgroup.broadinstitute.org/UKBB/</a>, and computed by Loh et al. 2018 Nat Genet. </li> </ul> <table> <tbody> <tr> <td> Phenotype </td> <td> Heritability estimate  </td> <td> Effective sample size </td> <td> Number of SNPs </td> </tr> <tr> <td> Height </td> <td> 0.570 </td> <td> 650K </td> <td> 12 Million </td> </tr> <tr> <td> Body mass index </td> <td> 0.303 </td> <td> 500K </td> <td> 12 Million </td> </tr> <tr> <td> Cardiovascular disease </td> <td> 0.155 </td> <td> 450K </td> <td> 12 Million </td> </tr> <tr> <td> Type 2 diabetes </td> <td> 0.073 </td> <td> 450K </td> <td> 12 Million </td> </tr> </tbody> </table>

opencc-by-4.0Jul 2023View details →

zenodo36/100

The Role of Criptic Ancestral Symmetry In Histone Folding Mechanisms Across Eukarya and Archaea

The shown folders contain the molecular dynamics simulation data, used tools, and scripts for the study of "The Role of Criptic Ancestral Symmetry In Histone Folding Mechanisms Across Eukarya and Archaea". The simulation data includes the force field and simulation setup for both AWSEM-MD and atomistic MD in OpenMM, the data analyses that are presented in the related paper, and the representative conformations from each simulation. Due to the large file size, the original trajectory files are available upon separate request. The tools and scripts folder includes the specific version of the AWSEM model, implemented in the LAMMPS package, and the scripts used to analyze the simulations. For detailed instructions on using AWSEM model, please refer to our Github: <a href="https://github.com/adavtyan/awsemmd/wiki">https://github.com/adavtyan/awsemmd/wiki</a>. For detailed instructions on using the LAMMPS package, please refer to <a href="https://www.lammps.org/#gsc.tab=0">https://www.lammps.org/#gsc.tab=0</a>. For detailed instructions on using the OpenMM package, please refer to <a href="https://openmm.org/">https://openmm.org/</a>. For any questions about using this data repository, please feel free to contact the author.

opencc-by-4.0Aug 2023View details →

dryad36/100

Archaeology demonstrates sustainable Ancestral Coast Salish salmon stewardship over thousands of years pre-contact

Salmon are an essential component of the ecosystem in Tsleil-Waututh Nation's traditional, ancestral, and unceded territory, centred on present-day Burrard Inlet, BC, Canada, where Tsleil-Waututh people have been harvesting salmon, along with a wide variety of other fishes, for millennia. Tsleil-Waututh Nation is an ancestral Coast Salish community that has called the Inlet home since time immemorial. This research assesses the continuity and sustainability of the salmon fishery at təmtəmíxʷtən, an ancestral Tsleil-Waututh settlement in the Inlet, over thousands of years before European contact (1792 CE). We apply Zooarchaeology by Mass Spectrometry (ZooMS) analysis to 245 archaeological salmon vertebrae to identify the species that were harvested by the Tsleil-Waututh community that lived at təmtəmíxʷtən. The results demonstrate that Tsleil-Waututh communities consistently and preferentially fished for chum salmon (Oncorhynchus keta) over the period of almost 3,000 years. The consistent abundance indicates a sustainable chum salmon fishery over that time and a strong salmon-to-people relationship through generations. This research supports Tsleil-Waututh Nation's stewardship obligations under their ancestral legal principles to maintain conditions that uphold the Nation's way of life.

opencc-zeroDec 2022View details →

zenodo36/100

FIGURE 5 Ancestral state reconstructions. A. Whorl count. B. Body length. C in Phylogeny and systematic revision of the helicarionid semislugs of eastern Queensland (Stylommatophora, Helicarionidae)

FIGURE 5 Ancestral state reconstructions. A. Whorl count. B. Body length. C. Altitude.

opencc-by-4.0Oct 2019View details →

dryad36/100