Author
David P. Mindell
Other affiliations: University of Cincinnati, University of Michigan, California Academy of Sciences
Bio: David P. Mindell is an academic researcher from University of California, San Francisco. The author has contributed to research in topics: Phylogenetic tree & Phylogenetics. The author has an hindex of 42, co-authored 78 publications receiving 9958 citations. Previous affiliations of David P. Mindell include University of Cincinnati & University of Michigan.
Topics: Phylogenetic tree, Phylogenetics, Monophyly, Genome, Molecular evolution
Papers published on a yearly basis
Papers
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Duke University1, University of Texas at Austin2, Heidelberg Institute for Theoretical Studies3, American Museum of Natural History4, Beijing Genomics Institute5, Xi'an Jiaotong University6, New Mexico State University7, University of Sydney8, University of California9, Uppsala University10, University of Copenhagen11, Okinawa Institute of Science and Technology12, University of Georgia13, Griffith University14, Catalan Institution for Research and Advanced Studies15, Joint Institute for Nuclear Research16, Oak Ridge National Laboratory17, Aarhus University18, Washington University in St. Louis19, University of California, Santa Cruz20, Cardiff University21, Kunming Institute of Zoology22, China Agricultural University23, Louisiana State University24, Tulane University25, Copenhagen Zoo26, Federal University of Pará27, Oregon Health & Science University28, Technical University of Denmark29, Canterbury Museum30, Curtin University31, Novosibirsk State University32, Smithsonian Institution33, National University of Singapore34, National Museum of Natural History35, Nova Southeastern University36, Occidental College37, University of Edinburgh38, Harvard University39, University of California, San Francisco40, University of Florida41, University of Illinois at Urbana–Champaign42
TL;DR: A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea.
Abstract: To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
1,624 citations
University of California, Berkeley1, Stanford University2, Spanish National Research Council3, University of New Mexico4, American Museum of Natural History5, University of California, Davis6, Simon Fraser University7, California Academy of Sciences8, University of Wisconsin-Madison9, University of California, San Francisco10, Missouri Botanical Garden11
TL;DR: Evidence that the global ecosystem as a whole is approaching a planetary-scale critical transition as a result of human influence is reviewed, highlighting the need to improve biological forecasting by detecting early warning signs of critical transitions.
Abstract: There is evidence that human influence may be forcing the global ecosystem towards a rapid, irreversible, planetary-scale shift into a state unknown in human experience. Most forecasts of how the biosphere will change in response to human activity are rooted in projecting trajectories. Such models tend not anticipate critical transitions or tipping points, although recent work indicates a high probability of those taking place. And, at a local scale, ecosystems are known to shift abruptly between states when critical thresholds are passed. These authors review the evidence from across ecology and palaeontology that such a transition is being approached on the scale of the entire biosphere. They go on to suggest how biological forecasting might be improved to allow us to detect early warning signs of critical transitions on a global, as well as local, scale. Localized ecological systems are known to shift abruptly and irreversibly from one state to another when they are forced across critical thresholds. Here we review evidence that the global ecosystem as a whole can react in the same way and is approaching a planetary-scale critical transition as a result of human influence. The plausibility of a planetary-scale ‘tipping point’ highlights the need to improve biological forecasting by detecting early warning signs of critical transitions on global as well as local scales, and by detecting feedbacks that promote such transitions. It is also necessary to address root causes of how humans are forcing biological changes.
1,571 citations
Beijing Genomics Institute1, University of Copenhagen2, Royal Veterinary College3, Seoul National University4, University of Nebraska–Lincoln5, University of Porto6, University of South Carolina7, Montclair State University8, Uppsala University9, National University of Singapore10, University of California, Berkeley11, South China University of Technology12, Chinese Academy of Sciences13, Kunming Institute of Zoology14, Howard Hughes Medical Institute15, Aberystwyth University16, University of Kent17, University of California, Riverside18, Mississippi State University19, Austral University of Chile20, Swedish University of Agricultural Sciences21, China Agricultural University22, Cardiff University23, Copenhagen Zoo24, Louisiana State University25, Washington University in St. Louis26, Xi'an Jiaotong University27, University of California, Santa Cruz28, Nova Southeastern University Oceanographic Center29, Smithsonian Conservation Biology Institute30, National Museum of Natural History31, Natural History Museum32, University of California, San Francisco33, Harvard University34, University of Florida35, University of Edinburgh36, New Mexico State University37, Macau University of Science and Technology38, Curtin University39
TL;DR: This work explored bird macroevolution using full genomes from 48 avian species representing all major extant clades to reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
Abstract: Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
872 citations
TL;DR: A PCR-based approach to sequencing complete mitochondrial genomes is described along with a set of 86 primers designed primarily for avian mitochondrial DNA, which should make available a wider variety of mitochondrial genes for studies based on smaller data sets.
739 citations
01 Jan 1997
TL;DR: This chapter discusses Phylogeny in Studies of Bird Ecology, Behavior, and Morphology, and the Relevance of Microevolutionary Processes to Higher Level Molecular Systematics.
Abstract: Molecular Sequences and Evolutionary History in Birds: T.W. Quinn, Molecular Evolution of the Mitochondrial Genome. D.B. McDonald and W.K. Potts, DNA Microsatellites as Genetic Markers at Several Scales. A.J. Baker and H.D. Marshall, Mitochondrial Control Region Sequences as Tools for Understanding Evolution. W.S. Moore and V.R. DeFilippis, The Window of Taxonomic Resolution for Phylogenies Based on Mitochondrial Cytochrome b. P. Houde, A. Cooper, E. Leslie, A.E. Strand, and G.A. Montano, Phylogeny and Evolution of of 12S rDNA in Gruiformes (Aves). D. Siegel-Causey, Phylogeny of the Pelacaniformes: Molecular Systematics of a Privative Group. K. Lee, J. Feinstein, and J. Cracraft, The Phylogeny of Ratite Birds: Resolving Conflicts between Molecular and Morphological Data Sets. D.P. Mindell, M.D. Sorenson, C.J. Huddleston, H.C. Miranda, Jr., A. Knight, S.J. Sawchuck, and T. Yuri, Phylogenetic Relationships among and within Select Avian Orders Based on Mitochondrial DNA. Applying Phylogeny and Population Genetics to Broader Issues: S.V. Edwards, Relevance of Microevolutionary Processes to Higher Level Molecular Systematics. F.H. Sheldon and L.A. Whittingham, Phylogeny in Studies of Bird Ecology, Behavior, and Morphology. R.M. Zink, Phylogeographic Studies of North American Birds. M.S. Roy, J.M. Cardoso da Silva, P. Arctander, J. Garcia-Moreno and J. Fjeldsa, The Speciation of South American and African Birds in Montane Regions. A. Cooper, Studies of Avian Ancient DNA: From Jurassic Park to Modern Island Extinctions. Chapter References. Subject Index.
384 citations
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28 Jul 2005
TL;DR: PfPMP1）与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。
18,940 citations
Journal Article•
TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
11,521 citations
Australian National University1, Stockholm Resilience Centre2, University of Copenhagen3, McGill University4, Stellenbosch University5, University of Wisconsin-Madison6, Wageningen University and Research Centre7, Stockholm University8, Royal Swedish Academy of Sciences9, Potsdam Institute for Climate Impact Research10, International Livestock Research Institute11, Commonwealth Scientific and Industrial Research Organisation12, University College London13, Stockholm Environment Institute14, The Energy and Resources Institute15, University of California, San Diego16, Royal Institute of Technology17
TL;DR: An updated and extended analysis of the planetary boundary (PB) framework and identifies levels of anthropogenic perturbations below which the risk of destabilization of the Earth system (ES) is likely to remain low—a “safe operating space” for global societal development.
Abstract: The planetary boundaries framework defines a safe operating space for humanity based on the intrinsic biophysical processes that regulate the stability of the Earth system. Here, we revise and update the planetary boundary framework, with a focus on the underpinning biophysical science, based on targeted input from expert research communities and on more general scientific advances over the past 5 years. Several of the boundaries now have a two-tier approach, reflecting the importance of cross-scale interactions and the regional-level heterogeneity of the processes that underpin the boundaries. Two core boundaries—climate change and biosphere integrity—have been identified, each of which has the potential on its own to drive the Earth system into a new state should they be substantially and persistently transgressed.
7,169 citations
01 Aug 2000
TL;DR: Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.
Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.
4,833 citations
Harvard University1, Stockholm Resilience Centre2, Potsdam Institute for Climate Impact Research3, University of Oxford4, City University London5, Chatham House6, World Wide Fund for Nature7, Environmental Change Institute8, University of California, Santa Barbara9, University of Minnesota10, CGIAR11, Johns Hopkins University12, American University of Beirut13, Wageningen University and Research Centre14, Institute for Health Metrics and Evaluation15, Indian Institute of Technology Kanpur16, ETH Zurich17, Commonwealth Scientific and Industrial Research Organisation18, University of Indonesia19, World Health Organization20, Food and Agriculture Organization21, International Food Policy Research Institute22, Royal Swedish Academy of Sciences23, University of Auckland24, Public Health Foundation of India25, Centre for Science and Environment26
TL;DR: Food in the Anthropocene : the EAT-Lancet Commission on healthy diets from sustainable food systems focuses on meat, fish, vegetables and fruit as sources of protein.
4,710 citations