Linda Goodman
A5066114837- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Genomics and Chromatin Dynamics
- Genetic diversity and population structure
- Bat Biology and Ecology Studies
- Archaeology and Natural History
- Diverse Musicological Studies
- Indigenous Studies and Ecology
- Marine animal studies overview
- Epigenetics and DNA Methylation
- RNA and protein synthesis mechanisms
- Music History and Culture
- Adipose Tissue and Metabolism
- Archaeology and ancient environmental studies
- Human-Animal Interaction Studies
- Yersinia bacterium, plague, ectoparasites research
- Evolution and Paleontology Studies
- Indigenous Health, Education, and Rights
- Metabolomics and Mass Spectrometry Studies
- Organic Food and Agriculture
- Molecular Biology Techniques and Applications
- Developmental Biology and Gene Regulation
- Wildlife Ecology and Conservation
- Animal Vocal Communication and Behavior
- Musicology and Musical Analysis
Fauna and Flora International
2023
Broad Institute
2018-2022
Stanford University
2018
Museum of New Mexico
1994
Behavioral genetics in dogs has focused on modern breeds, which are isolated subgroups with distinctive physical and, purportedly, behavioral characteristics. We interrogated breed stereotypes by surveying owners of 18,385 purebred and mixed-breed genotyping 2155 dogs. Most traits heritable [heritability ( h 2 ) > 25%], admixture patterns reveal propensities. Breed explains just 9% variation individuals. Genome-wide association analyses identify 11 loci that significantly associated...
Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes 240 species, we identify bases that, when mutated, are likely affect fitness and alter disease risk. At least 332 million (~10.7%) in human genome unusually conserved across species (evolutionarily constrained) relative neutrally evolving repeats, 4552 ultraconserved elements nearly perfectly conserved. Of 101 significantly constrained single bases, 80% outside protein-coding exons half...
Annotating coding genes and inferring orthologs are two classical challenges in genomics evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method integrates structural gene annotation orthology inference. implements different paradigm orthologous loci, improves ortholog detection of conserved compared with state-of-the-art methods, handles even highly fragmented assemblies. scales...
The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis genetic variation across an alignment 241 mammal genome assemblies, addressing prior concerns regarding limited genomic sampling species. compared neutral genome-wide phylogenomic signals using concatenation coalescent-based approaches, interrogated chromosomes, analyzed extensive catalogs structural variants. Interordinal...
Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability discern which positions functionally important. Evolutionary constraint is a powerful predictor function, agnostic cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% the genome as significantly constrained and likely functional. We compared annotation, association studies, copy-number variation,...
We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. found that although mammals resemble one another total and diversity, they show substantial differences with regard recent accumulation. This includes multiple expansion quiescence events across mammalian tree. Young TEs, particularly long interspersed elements, drive increases size, whereas DNA transposons are associated smaller genomes....
Human accelerated regions (HARs) are conserved genomic loci that evolved at an rate in the human lineage and may underlie human-specific traits. We generated HARs chimpanzee with automated pipeline alignment of 241 mammalian genomes. Combining deep learning chromatin capture experiments neural progenitor cells, we discovered a significant enrichment topologically associating domains containing variants change three-dimensional (3D) genome organization. Differential gene expression between...
Understanding the regulatory landscape of human genome is a long-standing objective modern biology. Using reference-free alignment across 241 mammalian genomes produced by Zoonomia Consortium, we charted evolutionary trajectories for 0.92 million candidate cis-regulatory elements (cCREs) and 15.6 transcription factor binding sites (TFBSs). We identified 439,461 cCREs 2,024,062 TFBSs under constraint. Genes near constrained perform fundamental cellular processes, whereas genes...
Species persistence can be influenced by the amount, type, and distribution of diversity across genome, suggesting a potential relationship between historical demography resilience. In this study, we surveyed genetic variation single genomes 240 mammals that compose Zoonomia alignment to evaluate how effective population size (
Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent functionally conserved despite low sequence conservation. We developed Tissue-Aware Conservation Inference Toolkit (TACIT) associate candidate with species' using predictions from machine learning...
Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) are enriched for brain functions across genetic, epigenomic, transcriptomic datasets. Using massively parallel reporter assays six cell types, we discovered 800 hCONDELs conferring significant differences regulatory activity, half of which enhance rather than disrupt function....
Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes syntenic relationships at 16 nodes along phylogeny. Three different reference genomes (human, sloth, cattle) phylogenetically distinct superorders were used assess bias in expand...
Vocal production learning ("vocal learning") is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from the Egyptian fruit bat (
Abstract Horizontal transfer of transposable elements (TEs) is an important mechanism contributing to genetic diversity and innovation. Bats (order Chiroptera) have repeatedly been shown experience horizontal TEs at what appears be a high rate compared with other mammals. We investigated the occurrence horizontally transferred (HT) DNA transposons involving bats. found over 200 putative HT within bats; 16 were shared across distantly related mammalian clades, 2 fish two lizard species. Our...
We reconstruct the phenotype of Balto, heroic sled dog renowned for transporting diphtheria antitoxin to Nome, Alaska, in 1925, using evolutionary constraint estimates from Zoonomia alignment 240 mammals and 682 genomes dogs wolves 21st century. Balto shares just part his diverse ancestry with eponymous Siberian husky breed. Balto’s genotype predicts a combination coat features atypical modern breeds, slightly smaller stature. He had enhanced starch digestion compared Greenland compendium...
Abstract Evolutionary constraint and acceleration are powerful, cell-type agnostic measures of functional importance. Previous studies in mammals were limited by species number reliance on human-referenced alignments. We explore the evolution placental mammals, including humans, through reference-free whole-genome alignment 240 protein-coding alignments for 428 species. estimate 10.7% human genome is evolutionarily constrained. resolve to single nucleotides, pinpointing positions, refine...
Current knowledge of cancer genomics remains biased against noncoding mutations. To systematically search for regulatory mutations, we assessed mutations in conserved positions the genome under assumption that these are more likely to be functional than with low conservation. this end, use whole-genome sequencing data from International Cancer Genome Consortium and combined it evolutionary constraint inferred 240 mammals, identify genes enriched (NCCMs), nature. We compare medulloblastoma...
Journal Article Singing the Songs of My Ancestors: The Life and Music Helma Swan, Makah Elder Get access Elder. By Goodman Linda J. Swan Helma. Foreword by Bill Holm. (Norman: University Oklahoma Press, 2003. xvii + 339 pp. Illustrations, maps, tables, glossary, appendixes, notes, bibliography, index. $44.95.) Victoria Lindsay Levine Colorado College Search for other works this author on: Oxford Academic Google Scholar Western Historical Quarterly, Volume 35, Issue 2, Summer 2004, Pages...
Many mammals have naturally evolved solutions to human biomedical problems. The genes and regulatory elements underlying their protective strategies are generally neither novel nor species-specific, but rather shared among all mammals, including humans. Adaptive physiology published in the literature provides a starting point identify species with natural disease resistance which genomic targets that can be translated therapeutics. When searching through available datasets for of interest...