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1. A genomic timescale for placental mammal evolution

Author

Foley, Nicole M, Mason, Victor C, Harris, Andrew J, Bredemeyer, Kevin R, Damas, Joana, Lewin, Harris A, Eizirik, Eduardo, Gatesy, John, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Springer, Mark S, Murphy, William J, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Fan, Kaili, Fanter, Cornelia, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, Steiner, Cynthia, Storer, Jessica M, Sullivan, Kevin AM, Sullivan, Patrick F, and Sundström, Elisabeth

Subjects
Genetics, Human Genome, Biotechnology, Animals, Female, Biological Evolution, Eutheria, Evolution, Molecular, Fossils, Genomics, Phylogeny, Genetic Variation, Time Factors, Zoonomia Consortium‡, General Science & Technology
Abstract

The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic time trees reveal an accumulation of cladogenic events before and immediately after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance and the K-Pg extinction in the placental radiation.

Published
2023

2. Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs

Author

Moon, Katherine L, Huson, Heather J, Morrill, Kathleen, Wang, Ming-Shan, Li, Xue, Srikanth, Krishnamoorthy, Lindblad-Toh, Kerstin, Svenson, Gavin J, Karlsson, Elinor K, Shapiro, Beth, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, Steiner, Cynthia, Storer, Jessica M, Sullivan, Kevin AM, Sullivan, Patrick F, Sundström, Elisabeth, Supple, Megan A, and Swofford, Ross

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Genetics, Animals, Dogs, Male, Genome, Genomics, Genotype, Phenotype, Wolves, Biodiversity, Genetic Variation, Zoonomia Consortium, General Science & Technology
Abstract

We reconstruct the phenotype of Balto, the heroic sled dog renowned for transporting diphtheria antitoxin to Nome, Alaska, in 1925, using evolutionary constraint estimates from the Zoonomia alignment of 240 mammals and 682 genomes from dogs and wolves of the 21st century. Balto shares just part of his diverse ancestry with the eponymous Siberian husky breed. Balto's genotype predicts a combination of coat features atypical for modern sled dog breeds, and a slightly smaller stature. He had enhanced starch digestion compared with Greenland sled dogs and a compendium of derived homozygous coding variants at constrained positions in genes connected to bone and skin development. We propose that Balto's population of origin, which was less inbred and genetically healthier than that of modern breeds, was adapted to the extreme environment of 1920s Alaska.

Published
2023

3. The contribution of historical processes to contemporary extinction risk in placental mammals

Author

Wilder, Aryn P, Supple, Megan A, Subramanian, Ayshwarya, Mudide, Anish, Swofford, Ross, Serres-Armero, Aitor, Steiner, Cynthia, Koepfli, Klaus-Peter, Genereux, Diane P, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Marques-Bonet, Tomas, Munoz Fuentes, Violeta, Foley, Kathleen, Meyer, Wynn K, Ryder, Oliver A, Shapiro, Beth, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Mason, Victor C, Meadows, Jennifer RS, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Smit, Arian FA, Springer, Mark, and Srinivasan, Chaitanya

Subjects
Biological Sciences, Evolutionary Biology, Genetics, Behavioral and Social Science, Human Genome, Basic Behavioral and Social Science, Life on Land, Animals, Female, Pregnancy, Eutheria, Extinction, Biological, Genetic Variation, Genome, Population Density, Risk, Zoonomia Consortium‡, General Science & Technology
Abstract

Species persistence can be influenced by the amount, type, and distribution of diversity across the genome, suggesting a potential relationship between historical demography and resilience. In this study, we surveyed genetic variation across single genomes of 240 mammals that compose the Zoonomia alignment to evaluate how historical effective population size (Ne) affects heterozygosity and deleterious genetic load and how these factors may contribute to extinction risk. We find that species with smaller historical Ne carry a proportionally larger burden of deleterious alleles owing to long-term accumulation and fixation of genetic load and have a higher risk of extinction. This suggests that historical demography can inform contemporary resilience. Models that included genomic data were predictive of species' conservation status, suggesting that, in the absence of adequate census or ecological data, genomic information may provide an initial risk assessment.

Published
2023

4. The functional and evolutionary impacts of human-specific deletions in conserved elements

Author

Xue, James R, Mackay-Smith, Ava, Mouri, Kousuke, Garcia, Meilin Fernandez, Dong, Michael X, Akers, Jared F, Noble, Mark, Li, Xue, Lindblad-Toh, Kerstin, Karlsson, Elinor K, Noonan, James P, Capellini, Terence D, Brennand, Kristen J, Tewhey, Ryan, Sabeti, Pardis C, Reilly, Steven K, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Lind, Abigail, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Schäffer, Daniel E, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, and Steiner, Cynthia

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Neurosciences, Human Genome, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Neurological, Humans, Conserved Sequence, Evolution, Molecular, Genome, Genomics, RNA-Binding Proteins, Sequence Deletion, Brain, Gene Expression Regulation, Developmental, Zoonomia Consortium†, General Science & Technology
Abstract

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) deletions are enriched for human brain functions across genetic, epigenomic, and transcriptomic datasets. Using massively parallel reporter assays in six cell types, we discovered 800 hCONDELs conferring significant differences in regulatory activity, half of which enhance rather than disrupt regulatory function. We highlight several hCONDELs with putative human-specific effects on brain development, including HDAC5, CPEB4, and PPP2CA. Reverting an hCONDEL to the ancestral sequence alters the expression of LOXL2 and developmental genes involved in myelination and synaptic function. Our data provide a rich resource to investigate the evolutionary mechanisms driving new traits in humans and other species.

Published
2023

5. Integrating gene annotation with orthology inference at scale

Author

Kirilenko, Bogdan M, Munegowda, Chetan, Osipova, Ekaterina, Jebb, David, Sharma, Virag, Blumer, Moritz, Morales, Ariadna E, Ahmed, Alexis-Walid, Kontopoulos, Dimitrios-Georgios, Hilgers, Leon, Lindblad-Toh, Kerstin, Karlsson, Elinor K, Hiller, Michael, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, Steiner, Cynthia, Storer, Jessica M, Sullivan, Kevin AM, and Sullivan, Patrick F

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Generic health relevance, Animals, Female, Mice, Eutheria, Genome, Genomics, Molecular Sequence Annotation, Birds, Zoonomia Consortium‡, General Science & Technology
Abstract

Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method that integrates structural gene annotation and orthology inference. TOGA implements a different paradigm to infer orthologous loci, improves ortholog detection and annotation of conserved genes compared with state-of-the-art methods, and handles even highly fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 501 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. TOGA is a powerful and scalable method to annotate and compare genes in the genomic era.

Published
2023

6. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning

Author

Kaplow, Irene M, Lawler, Alyssa J, Schäffer, Daniel E, Srinivasan, Chaitanya, Sestili, Heather H, Wirthlin, Morgan E, Phan, BaDoi N, Prasad, Kavya, Brown, Ashley R, Zhang, Xiaomeng, Foley, Kathleen, Genereux, Diane P, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Meyer, Wynn K, Pfenning, Andreas R, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, and Steiner, Cynthia

Subjects
Biological Sciences, Genetics, Pediatric, Human Genome, Rare Diseases, Congenital Structural Anomalies, Underpinning research, 1.1 Normal biological development and functioning, Neurological, Mental health, Animals, Enhancer Elements, Genetic, Genetic Variation, Machine Learning, Mammals, Phenotype, Zoonomia Consortium**, General Science & Technology
Abstract

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 between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.

Published
2023

7. Three-dimensional genome rewiring in loci with human accelerated regions

Author

Keough, Kathleen C, Whalen, Sean, Inoue, Fumitaka, Przytycki, Pawel F, Fair, Tyler, Deng, Chengyu, Steyert, Marilyn, Ryu, Hane, Lindblad-Toh, Kerstin, Karlsson, Elinor, Nowakowski, Tomasz, Ahituv, Nadav, Pollen, Alex, Pollard, Katherine S, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Genereux, Diane P, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Karlsson, Elinor K, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, Ryan, Louise, Ryder, Oliver A, Sabeti, Pardis C, Schäffer, Daniel E, Serres, Aitor, Shapiro, Beth, Smit, Arian FA, Springer, Mark, Srinivasan, Chaitanya, Steiner, Cynthia, Storer, Jessica M, and Sullivan, Kevin AM

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Stem Cell Research, Human Genome, Biotechnology, Underpinning research, 1.1 Normal biological development and functioning, Animals, Humans, Chromatin, Genome, Human, Genomics, Pan troglodytes, Genetic Loci, Neurogenesis, Deep Learning, Zoonomia Consortium§, General Science & Technology
Abstract

Human accelerated regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with an automated pipeline and an alignment of 241 mammalian genomes. Combining deep learning with chromatin capture experiments in human and chimpanzee neural progenitor cells, we discovered a significant enrichment of HARs in topologically associating domains containing human-specific genomic variants that change three-dimensional (3D) genome organization. Differential gene expression between humans and chimpanzees at these loci suggests rewiring of regulatory interactions between HARs and neurodevelopmental genes. Thus, comparative genomics together with models of 3D genome folding revealed enhancer hijacking as an explanation for the rapid evolution of HARs.

Published
2023

8. Leveraging base-pair mammalian constraint to understand genetic variation and human disease

Author

Sullivan, Patrick F, Meadows, Jennifer RS, Gazal, Steven, Phan, BaDoi N, Li, Xue, Genereux, Diane P, Dong, Michael X, Bianchi, Matteo, Andrews, Gregory, Sakthikumar, Sharadha, Nordin, Jessika, Roy, Ananya, Christmas, Matthew J, Marinescu, Voichita D, Wang, Chao, Wallerman, Ola, Xue, James, Yao, Shuyang, Sun, Quan, Szatkiewicz, Jin, Wen, Jia, Huckins, Laura M, Lawler, Alyssa, Keough, Kathleen C, Zheng, Zhili, Zeng, Jian, Wray, Naomi R, Li, Yun, Johnson, Jessica, Chen, Jiawen, Paten, Benedict, Reilly, Steven K, Hughes, Graham M, Weng, Zhiping, Pollard, Katherine S, Pfenning, Andreas R, Forsberg-Nilsson, Karin, Karlsson, Elinor K, Lindblad-Toh, Kerstin, Armstrong, Joel C, Birren, Bruce W, Bredemeyer, Kevin R, Breit, Ana M, Clawson, Hiram, Damas, Joana, Di Palma, Federica, Diekhans, Mark, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Garcia, Carlos J, Gatesy, John, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Johnson, Jeremy, Juan, David, Kaplow, Irene M, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Lewin, Harris A, Lind, Abigail, Mackay-Smith, Ava, Marques-Bonet, Tomas, Mason, Victor C, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, and Navarro, Arcadi

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Clinical Research, Human Genome, Brain Disorders, Generic health relevance, Animals, Humans, Biological Evolution, Genetic Variation, Genome, Human, Genome-Wide Association Study, Genomics, Molecular Sequence Annotation, Polymorphism, Single Nucleotide, Disease, Zoonomia Consortium§, General Science & Technology
Abstract

Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.

Published
2023

9. Evolution of the ancestral mammalian karyotype and syntenic regions

Author

Damas, Joana, Corbo, Marco, Kim, Jaebum, Turner-Maier, Jason, Farré, Marta, Larkin, Denis M, Ryder, Oliver A, Steiner, Cynthia, Houck, Marlys L, Hall, Shaune, Shiue, Lily, Thomas, Stephen, Swale, Thomas, Daly, Mark, Korlach, Jonas, Uliano-Silva, Marcela, Mazzoni, Camila J, Birren, Bruce W, Genereux, Diane P, Johnson, Jeremy, Lindblad-Toh, Kerstin, Karlsson, Elinor K, Nweeia, Martin T, Johnson, Rebecca N, Lewin, Harris A, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Bredemeyer, Kevin R, Breit, Ana M, Christmas, Matthew J, Clawson, Hiram, Di Palma, Federica, Diekhans, Mark, Dong, Michael X, Eizirik, Eduardo, Fan, Kaili, Fanter, Cornelia, Foley, Nicole M, Forsberg-Nilsson, Karin, Garcia, Carlos J, Gatesy, John, Gazal, Steven, Goodman, Linda, Grimshaw, Jenna, Halsey, Michaela K, Harris, Andrew J, Hickey, Glenn, Hiller, Michael, Hindle, Allyson G, Hubley, Robert M, Hughes, Graham M, Juan, David, Kaplow, Irene M, Keough, Kathleen C, Kirilenko, Bogdan, Koepfli, Klaus-Peter, Korstian, Jennifer M, Kowalczyk, Amanda, Kozyrev, Sergey V, Lawler, Alyssa J, Lawless, Colleen, Lehmann, Thomas, Levesque, Danielle L, Li, Xue, Lind, Abigail, Mackay-Smith, Ava, Marinescu, Voichita D, Marques-Bonet, Tomas, Mason, Victor C, Meadows, Jennifer RS, Meyer, Wynn K, Moore, Jill E, Moreira, Lucas R, Moreno-Santillan, Diana D, Morrill, Kathleen M, Muntané, Gerard, Murphy, William J, Navarro, Arcadi, Nweeia, Martin, Ortmann, Sylvia, Osmanski, Austin, Paten, Benedict, Paulat, Nicole S, Pfenning, Andreas R, Phan, BaDoi N, Pollard, Katherine S, Pratt, Henry E, Ray, David A, Reilly, Steven K, Rosen, Jeb R, Ruf, Irina, and Ryan, Louise

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Evolutionary Biology, Genetics, Human Genome, 1.1 Normal biological development and functioning, Generic health relevance, Animals, Cattle, Chromosomes, Mammalian, Eutheria, Evolution, Molecular, Humans, Karyotype, Mammals, Phylogeny, Sloths, Synteny, chromosome evolution, mammals, synteny conservation, ancestral genome reconstruction, topologically associating domains, Zoonomia Consortium
Abstract

Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes and syntenic relationships at 16 nodes along the mammalian phylogeny. Three different reference genomes (human, sloth, and cattle) representing phylogenetically distinct mammalian superorders were used to assess reference bias in the reconstructed ancestral karyotypes and to expand the number of clades with reconstructed genomes. The mammalian ancestor likely had 19 pairs of autosomes, with nine of the smallest chromosomes shared with the common ancestor of all amniotes (three still conserved in extant mammals), demonstrating a striking conservation of synteny for ∼320 My of vertebrate evolution. The numbers and types of chromosome rearrangements were classified for transitions between the ancestral mammalian karyotype, descendent ancestors, and extant species. For example, 94 inversions, 16 fissions, and 14 fusions that occurred over 53 My differentiated the therian from the descendent eutherian ancestor. The highest breakpoint rate was observed between the mammalian and therian ancestors (3.9 breakpoints/My). Reconstructed mammalian ancestor chromosomes were found to have distinct evolutionary histories reflected in their rates and types of rearrangements. The distributions of genes, repetitive elements, topologically associating domains, and actively transcribed regions in multispecies homologous synteny blocks and evolutionary breakpoint regions indicate that purifying selection acted over millions of years of vertebrate evolution to maintain syntenic relationships of developmentally important genes and regulatory landscapes of gene-dense chromosomes.

Published
2022

13. Ash plume properties retrieved from infrared images: a forward and inverse modeling approach

Author

Cerminara, Matteo, Ongaro, Tomaso Esposti, Valade, Sébastien, and Harris, Andrew J. L.

Subjects
Physics - Geophysics, Physics - Atmospheric and Oceanic Physics, Physics - Data Analysis, Statistics and Probability, Physics - Fluid Dynamics, Physics - Instrumentation and Detectors, 76T15, 78-05, 86-02, 86-05, 86-08
Abstract

We present a coupled fluid-dynamic and electromagnetic model for volcanic ash plumes. In a forward approach, the model is able to simulate the plume dynamics from prescribed input flow conditions and generate the corresponding synthetic thermal infrared (TIR) image, allowing a comparison with field-based observations. An inversion procedure is then developed to retrieve ash plume properties from TIR images. The adopted fluid-dynamic model is based on a one-dimensional, stationary description of a self-similar (top-hat) turbulent plume, for which an asymptotic analytical solution is obtained. The electromagnetic emission/absorption model is based on the Schwarzschild's equation and on Mie's theory for disperse particles, assuming that particles are coarser than the radiation wavelength and neglecting scattering. [...] Application of the inversion procedure to an ash plume at Santiaguito volcano (Guatemala) has allowed us to retrieve the main plume input parameters, namely the initial radius $b_0$, velocity $U_0$, temperature $T_0$, gas mass ratio $n_0$, entrainment coefficient $k$ and their related uncertainty. Moreover, coupling with the electromagnetic model, we have been able to obtain a reliable estimate of the equivalent Sauter diameter $d_s$ of the total particle size distribution. The presented method is general and, in principle, can be applied to the spatial distribution of particle concentration and temperature obtained by any fluid-dynamic model, either integral or multidimensional, stationary or time-dependent, single or multiphase. The method discussed here is fast and robust, thus indicating potential for applications to real-time estimation of ash mass flux and particle size distribution, which is crucial for model-based forecasts of the volcanic ash dispersal process., Comment: 41 pages, 13 figures, submitted paper

Published
2014
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18. A genomic timescale for placental mammal evolution

Author

Foley, Nicole M., Mason, Victor C., Harris, Andrew J., Bredemeyer, Kevin R., Damas, Joana, Lewin, Harris A., Eizirik, Eduardo, Gatesy, John, Karlsson, Elinor K., Lindblad-Toh, Kerstin, Zoonomia Consortium, Zoonomia Consortium, Springer, Mark S., Murphy, William J., Foley, Nicole M., Mason, Victor C., Harris, Andrew J., Bredemeyer, Kevin R., Damas, Joana, Lewin, Harris A., Eizirik, Eduardo, Gatesy, John, Karlsson, Elinor K., Lindblad-Toh, Kerstin, Zoonomia Consortium, Zoonomia Consortium, Springer, Mark S., and Murphy, William J.

Abstract

The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic time trees reveal an accumulation of cladogenic events before and immediately after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance and the K-Pg extinction in the placental radiation.

Published
2023
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23. VIGIA: A Thermal and Visible Imagery System to Track Volcanic Explosions

Author

Vásconez, Freddy, primary, Moussallam, Yves, additional, Harris, Andrew J. L., additional, Latchimy, Thierry, additional, Kelfoun, Karim, additional, Bontemps, Martial, additional, Macías, Carlos, additional, Hidalgo, Silvana, additional, Córdova, Jorge, additional, Battaglia, Jean, additional, Mejía, Jessica, additional, Arrais, Santiago, additional, Vélez, Luis, additional, and Ramos, Cristina, additional

Published
2022
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29. Lava flow hazard map of Piton de la Fournaise volcano

Author

Chevrel, Magdalena Oryaëlle, primary, Favalli, Massimiliano, additional, Villeneuve, Nicolas, additional, Harris, Andrew J. L., additional, Fornaciai, Alessandro, additional, Richter, Nicole, additional, Derrien, Allan, additional, Boissier, Patrice, additional, Di Muro, Andrea, additional, and Peltier, Aline, additional

Published
2021
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30. Multi-parametric field experiment links explosive activity and persistent degassing at Stromboli

Author

Thivet, Simon, Harris, Andrew J. L., Gurioli, Lucia, Bani, Philipson, Observatoire de Physique du Globe de Clermont-Ferrand (OPGC), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Laboratoire Magmas et Volcans (LMV), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement et la société-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)-Observatoire de Physique du Globe de Clermont-Ferrand (OPGC), and Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)

Subjects
Strombolian explosions, [SDU]Sciences of the Universe [physics], [SDU.STU.VO]Sciences of the Universe [physics]/Earth Sciences/Volcanology, Gas flux, Particle size distribution, Persistent degassing, real- time monitoring, pyroclast mass flux
Abstract

International audience; A multi-parametric experiment at Stromboli volcano (Aeolian Islands, Italy) was installed in July 2016 focusing on the normal explosive activity and persistent degassing. A FLIR thermal camera, an UV SO₂ camera and a scanning DOAS, were deployed to record pyroclast and SO2 masses emitted during individual explosions, as well as persistent SO₂ fluxes, respectively. An ASHER instrument was also deployed in order to collect ash fallouts and to measure the grain size distribution of the samples. SO2 measurements confirm that persistent degassing was far greater than that emitted during the explosions. Further, we found that the data could be characterized by two periods. In the first period (25-27 July), activity was mainly characterized by gas-dominated (type 0) explosions, characterized by high velocity jets. Pyroclast mass fluxes were relatively low (280 kg/event on average), while persistent SO2 fluxes were high (274 t/d on average). In the second period (29-30 July), activity was mainly characterized by particle-loaded (type 1) explosions, characterized by velocity jets. Pyroclast mass fluxes were almost ten times higher (2400 kg/event on average), while persistent gas fluxes were significantly lower (82 t/d on average). Ash characterization also indicates that type 0 explosions fragments were characterized by a larger proportion of non-juvenile material compared to type 1 explosions fragments. These data suggest that Stromboli's type 1 explosions can be associated with low levels of degassing and the mass of particles accompanying such explosive events depends on the volume of a degassed magma cap sitting at the head of the magma column. This could make the classic particle-loaded explosions of Stromboli an aside from the true eruptive state of the volcano. Instead, gas-dominated explosions can be associated with high levels of degassing and are indicative of a highly-charged (with gas) system. We thus suggest that relatively deep magmatic processes, such as persistent degassing and slug formation can rapidly influence the superficial behavior of the eruptive conduit, modulating the presence or absence of degassed magma at the explosion/fragmentation level.

Published
2021
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42. Ultracontinuous Single Haplotype Genome Assemblies for the Domestic Cat (Felis catus) and Asian Leopard Cat (Prionailurus bengalensis).

Author

Bredemeyer, Kevin R, Harris, Andrew J, Li, Gang, Zhao, Le, Foley, Nicole M, Roelke-Parker, Melody, O'Brien, Stephen J, Lyons, Leslie A, Warren, Wesley C, and Murphy, William J

Subjects
*CATS, *FELIDAE, *CHROMOSOME inversions, *GENOMES, *PETS, *HAPLOTYPES
Abstract

In addition to including one of the most popular companion animals, species from the cat family Felidae serve as a powerful system for genetic analysis of inherited and infectious disease, as well as for the study of phenotypic evolution and speciation. Previous diploid-based genome assemblies for the domestic cat have served as the primary reference for genomic studies within the cat family. However, these versions suffered from poor resolution of complex and highly repetitive regions, with substantial amounts of unplaced sequence that is polymorphic or copy number variable. We sequenced the genome of a female F1 Bengal hybrid cat, the offspring of a domestic cat (Felis catus) x Asian leopard cat (Prionailurus bengalensis) cross, with PacBio long sequence reads and used Illumina sequence reads from the parents to phase >99.9% of the reads into the 2 species' haplotypes. De novo assembly of the phased reads produced highly continuous haploid genome assemblies for the domestic cat and Asian leopard cat, with contig N50 statistics exceeding 83 Mb for both genomes. Whole-genome alignments reveal the Felis and Prionailurus genomes are colinear, and the cytogenetic differences between the homologous F1 and E4 chromosomes represent a case of centromere repositioning in the absence of a chromosomal inversion. Both assemblies offer significant improvements over the previous domestic cat reference genome, with a 100% increase in contiguity and the capture of the vast majority of chromosome arms in 1 or 2 large contigs. We further demonstrated that comparably accurate F1 haplotype phasing can be achieved with members of the same species when one or both parents of the trio are not available. These novel genome resources will empower studies of feline precision medicine, adaptation, and speciation. [ABSTRACT FROM AUTHOR]

Published
2021
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43. Lava flow hazard map of Piton de la Fournaise volcano.

Author

Oryaëlle Chevrel, Magdalena, Favalli, Massimiliano, Villeneuve, Nicolas, Harris, Andrew J. L., Fornaciai, Alessandro, Richter, Nicole, Derrien, Allan, Boissier, Patrice, Di Muro, Andrea, and Peltier, Aline

Subjects
LAVA flows, VOLCANOES, VOLCANIC fields, HAZARDS, FLOW simulations, VOLCANIC eruptions, HAZARD mitigation
Abstract

Piton de la Fournaise, situated on La Réunion Island (France), is one of the most active hot spot basaltic shield volcanoes worldwide, experiencing at least two eruptions per year since the establishment of the observatory in 1979. Eruptions are typically fissure-fed and form extensive lava flow fields. About 95 % of some ~250 historical events (since the first confidently dated eruption in 1708) have occurred inside an uninhabited horse-shoe shaped caldera (hereafter referred to as the Enclos) which is open to the ocean on its eastern side. Rarely (12 times since the 18th century), fissures have opened outside of the Enclos where housing units, population centers and infrastructure are at risk. In such a situation, lava flow hazard maps are a useful way of visualizing lava flow inundation probabilities over large areas. Here, we present a lava flow hazard map for Piton de la Fournaise volcano based on: i) vent distribution, ii) statistics of lava flow lengths, iii) lava flow recurrence times, and iv) simulations of lava flow paths across multi-temporal (i.e., regularly updated) topography using the DOWNFLOW stochastic numerical model. A map of the entire volcano highlights that the most probable (up to 12 %) location for future lava flow inundation is within the Enclos, where about 100,000 visitors are present each year. Hazard distribution changes throughout the analysis period due to the high frequency of eruptions that constantly modifies the vent opening distribution as well as the topography and the lava flow dimensional characteristics. Outside of the Enclos, probabilities reach 0.5 % along the well-defined rift zones and, although hazard occurrence in inhabited areas is deemed to be very low (< 0.1 %), it may be underestimated here, as our study is only based on post-18th century records and neglects cycles of activity at the volcano. Specific hazard maps considering different event scenarios (i.e., events fed by different combinations of temporally evolving superficial and deep sources) are required to better assess affected areas in the future - especially by atypical, but potentially extremely hazardous, large volume eruptions. At such an active site, our method supports the need for regular updates of DEMs and associated lava flow hazard maps if we are to be effective in mitigating the associated risks. [ABSTRACT FROM AUTHOR]

Published
2020
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44. The viscosity of pāhoehoe lava: In situ syn-eruptive measurements from Kilauea, Hawaii

Author

Chevrel, Magdalena Oryaëlle, Harris, Andrew J. L., James, Michael Richard, Calabrò, Laura, Gurioli, Lucia, Pinkerton, Henry, Chevrel, Magdalena Oryaëlle, Harris, Andrew J. L., James, Michael Richard, Calabrò, Laura, Gurioli, Lucia, and Pinkerton, Henry

Abstract

Viscosity is one of the most important physical properties controlling lava flow dynamics. Usually, viscosity is measured in the laboratory where key parameters can be controlled but can never reproduce the natural environment and original state of the lava in terms of crystal and bubble contents, dissolved volatiles, and oxygen fugacity. The most promising approach for quantifying the rheology of molten lava in its natural state is therefore to carry out direct field measurements by inserting a viscometer into the lava while it is flowing. Such in-situ syn-eruptive viscosity measurements are notoriously difficult to perform due to the lack of appropriate instrumentation and the difficulty of working on or near an active lava flow. In the field, rotational viscometer measurements are of particular value as they have the potential to measure the properties of the flow interior rather than an integration of the viscosity of the viscoelastic crust + flow interior. To our knowledge only one field rotational viscometer is available, but logistical constraints have meant that it has not been used for 20 years. Here, we describe new viscosity measurements made using the refurbished version of this custom-built rotational viscometer, as performed on active pāhoehoe lobes from the 61G lava flow of Kilauea’s Pu’u ‘Ō‘ō eruption in 2016. We successfully measured a viscosity of ~380 Pa s at strain-rates between 1.6 and 5 s-1 28 and at 1144 °C. Additionally, synchronous lava sampling allowed us to provide detailed textural and chemical characterization of quenched samples. Application of current physico-chemical models based on this characterization (16±4 vol.% crystals; 50±6 vol.% vesicles), gave viscosity estimates that were approximately compatible with the measured values, highlighting the sensitivity of model-based viscosity estimates on the effect of deformable bubbles. Our measurements also agree on the range of viscosities in comparison to previous field experiments on Ha

Published
2018

45. Sex offending and serious mental illness: directions for policy and research

Author

Harris, Andrew J., Fisher, William, Veysey, Bonita M., Ragusa, Laura M., and Lurigio, Arthur J.

Subjects
Sex offenders -- Psychological aspects, Insane, Criminal and dangerous -- Care and treatment, Insane, Criminal and dangerous -- Research, Law, Psychology and mental health
Abstract

Over the past decade, two rapidly evolving areas of criminal justice practice have garnered increasing attention from policy makers, practitioners, and researchers: the management and treatment of justice involved individuals with serious and persistent mental illness, and the challenges of managing the perceived societal risk presented by sex offenders. Yet, whereas each of these issues has independently attracted significant attention, the nexus between them has remained largely unexamined. Matters of concern include the manner in which individuals with serious mental illness may be disproportionately affected by the expanding range of restrictions placed on those with sexual offense histories, the demands for adapting traditional models of sex offender treatment and supervision for those with serious mental illness, and the manner in which public mental health agencies must adapt their systems of inpatient and community-based care to meet the needs of clients with sex offense histories. This article explores the connections between sex offending and serious mental illness, examining the magnitude and nature of the issue, the organizational and programmatic challenges facing both the public mental health and criminal justice systems, and the emergent public policy implications. The article analyzes existing research, identifies relevant gaps in our existing body of knowledge, and concludes by presenting an agenda for policy makers and researchers.

Published
2010

46. Widening the net: the effects of transitioning to the Adam Walsh Act's federally mandated sex offender classification system

Author

Harris, Andrew J., Lobanov-Rostovsky, Christopher, and Levenson, Jill S.

Subjects
Community notification laws -- Influence, Sex offenders -- Identification and classification, Law, Psychology and mental health, Adam Walsh Child Protection and Safety Act
Abstract

With the 2006 passage of the Adam Walsh Child Protection and Safety Act (AWA), the U.S. Congress set forth a range of minimum standards governing the operation of sex offender registration and notification (SORN) systems throughout the nation. Many of these standards are based on the AWA's uniform system of registrant classification, which distinguishes registrants solely based on offense history and the nature of the conviction offense, without regard for additional risk factors. The current study evaluates the impact of the federal registration classification system on the distribution of individuals within state sex offender registries, specifically drawing on the experiences of Ohio and Oklahoma, two of the first states to undertake a reclassification of their registrant populations under the new federal guidelines. The findings indicate that the federal reclassification process produces a redistribution of registrants from lower SORN levels to higher ones and reveals statistically significant differences between newly reclassified 'high-risk' individuals and those designated as high risk under prior registration classification systems. Findings also suggest that juveniles and those potentially subject to AWA's retroactivity provisions may be disproportionately placed into the highest SORN tiers. Implications of these findings for practice and public policy are discussed.

Published
2010

48. Geology, tectonics, and the 2002-2003 eruption of the Semeru volcano, Indonesia: interpreted from high-spatial resolution satellite imagery

Author

Solikhin, Akhmad, Thouret, Jean-Claude, Gupta, Avijit, Harris, Andrew J L, Liew, Soo Chin, Solikhin, Akhmad, Thouret, Jean-Claude, Gupta, Avijit, Harris, Andrew J L, and Liew, Soo Chin

Abstract

The paper illustrates the application of high-spatial resolution satellite images in interpreting volcanic structures and eruption impacts in the Tengger–Semeru massif in east Java, Indonesia. We use high-spatial resolution images (IKONOS and SPOT 5) and aerial photos in order to analyze the structures of Semeru volcano and map the deposits. Geological and tectonic mapping is based on two DEMs and on the interpretation of aerial photos and four SPOT and IKONOS optical satellite images acquired between 1996 and 2002. We also compared two thermal Surface Kinetic Temperature ASTER images before and after the 2002–2003 eruption in order to delineate and evaluate the impacts of the pyroclastic density currents. Semeru's principal structural features are probably due to the tectonic setting of the volcano. A structural map of the Tengger–Semeru massif shows four groups of faults orientated N40, N160, N75, and N105 to N140. Conspicuous structures, such as the SE-trending horseshoe-shaped scar on Semeru's summit cone, coincide with the N160-trending faults. The direction of minor scars on the east flank parallels the first and second groups of faults. The Semeru composite cone hosts the currently active Jonggring-Seloko vent. This is located on, and buttressed against, the Mahameru edifice at the head of a large scar that may reflect a failure plane at shallow depth. Dipping 35° towards the SE, this failure plane may correspond to a weak basal layer of weathered volcaniclastic rocks of Tertiary age. We suggest that the deformation pattern of Semeru and its large scar may be induced by flank spreading over the weak basal layer of the volcano. It is therefore necessary to consider the potential for flank and summit collapse in the future. The last major eruption took place in December 2002–January 2003, and involved emplacement of block-and-ash flows. We have used the 2003 ASTER Surface Kinetic Temperature image to map the 2002–2003 pyroclastic density current deposits. We ha

Published
2012

50. Pāhoehoe flow cooling, discharge and coverage rates from thermal image chronometry.

Author

Harris, Andrew J. L., Dehn, Jonathan, James, Mike R., Hamilton, Christopher, Herd, Richard, Lodato, Luigi, Steffke, Andrea, Harris, Andrew J. L., Dehn, Jonathan, James, Mike R., Hamilton, Christopher, Herd, Richard, Lodato, Luigi, and Steffke, Andrea

Abstract

Theoretically- and empirically-derived cooling rates for active pāhoehoe lava flows show that surface cooling is controlled by conductive heat loss through a crust that is thickening with the square root of time. The model is based on a linear relationship that links log(time) with surface cooling. This predictable cooling behavior can be used assess the age of recently emplaced sheet flows from their surface temperatures. Using a single thermal image, or image mosaic, this allows quantification of the variation in areal coverage rates and lava discharge rates over 48 hour periods prior to image capture. For pāhoehoe sheet flow at Kīlauea (Hawai`i) this gives coverage rates of 1–5 m2/min at discharge rates of 0.01–0.05 m3/s, increasing to ∼40 m2/min at 0.4–0.5 m3/s. Our thermal chronometry approach represents a quick and easy method of tracking flow advance over a three-day period using a single, thermal snap-shot.

Published
2007

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