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Gill BA, Kondratieff BC, Casner KL, Encalada AC, Flecker AS, Gannon DG, Ghalambor CK, Guayasamin JM, Poff NL, Simmons MP, Thomas SA, Zamudio KR, Funk WC. Cryptic species diversity reveals biogeographic support for the 'mountain passes are higher in the tropics' hypothesis. Proc Biol Sci 2016; 283:20160553. [PMID: 27306051 PMCID: PMC4920318 DOI: 10.1098/rspb.2016.0553] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/18/2016] [Indexed: 01/30/2023] Open
Abstract
The 'mountain passes are higher in the tropics' (MPHT) hypothesis posits that reduced climate variability at low latitudes should select for narrower thermal tolerances, lower dispersal and smaller elevational ranges compared with higher latitudes. These latitudinal differences could increase species richness at low latitudes, but that increase may be largely cryptic, because physiological and dispersal traits isolating populations might not correspond to morphological differences. Yet previous tests of the MPHT hypothesis have not addressed cryptic diversity. We use integrative taxonomy, combining morphology (6136 specimens) and DNA barcoding (1832 specimens) to compare the species richness, cryptic diversity and elevational ranges of mayflies (Ephemeroptera) in the Rocky Mountains (Colorado; approx. 40°N) and the Andes (Ecuador; approx. 0°). We find higher species richness and smaller elevational ranges in Ecuador than Colorado, but only after quantifying and accounting for cryptic diversity. The opposite pattern is found when comparing diversity based on morphology alone, underscoring the importance of uncovering cryptic species to understand global biodiversity patterns.
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Affiliation(s)
- B A Gill
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
| | - B C Kondratieff
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - K L Casner
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - A C Encalada
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, 17-1200-841 Quito, Ecuador
| | - A S Flecker
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - D G Gannon
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - C K Ghalambor
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
| | - J M Guayasamin
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, 17-1200-841 Quito, Ecuador Centro de Investigación de la Biodiversidad y Cambio Climático, Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, Calle Machala y Sabanilla, Quito, Ecuador
| | - N L Poff
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
| | - M P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - S A Thomas
- School of Natural Resources, University of Nebraska, Lincoln, NE 68583, USA
| | - K R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - W C Funk
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
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Simmons MP, Bachy C, Sudek S, van Baren MJ, Sudek L, Ares M, Worden AZ. Intron Invasions Trace Algal Speciation and Reveal Nearly Identical Arctic and Antarctic Micromonas Populations. Mol Biol Evol 2015; 32:2219-35. [PMID: 25998521 PMCID: PMC4540971 DOI: 10.1093/molbev/msv122] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Spliceosomal introns are a hallmark of eukaryotic genes that are hypothesized to play important roles in genome evolution but have poorly understood origins. Although most introns lack sequence homology to each other, new families of spliceosomal introns that are repeated hundreds of times in individual genomes have recently been discovered in a few organisms. The prevalence and conservation of these introner elements (IEs) or introner-like elements in other taxa, as well as their evolutionary relationships to regular spliceosomal introns, are still unknown. Here, we systematically investigate introns in the widespread marine green alga Micromonas and report new families of IEs, numerous intron presence–absence polymorphisms, and potential intron insertion hot-spots. The new families enabled identification of conserved IE secondary structure features and establishment of a novel general model for repetitive intron proliferation across genomes. Despite shared secondary structure, the IE families from each Micromonas lineage bear no obvious sequence similarity to those in the other lineages, suggesting that their appearance is intimately linked with the process of speciation. Two of the new IE families come from an Arctic culture (Micromonas Clade E2) isolated from a polar region where abundance of this alga is increasing due to climate induced changes. The same two families were detected in metagenomic data from Antarctica—a system where Micromonas has never before been reported. Strikingly high identity between the Arctic isolate and Antarctic coding sequences that flank the IEs suggests connectivity between populations in the two polar systems that we postulate occurs through deep-sea currents. Recovery of Clade E2 sequences in North Atlantic Deep Waters beneath the Gulf Stream supports this hypothesis. Our research illuminates the dynamic relationships between an unusual class of repetitive introns, genome evolution, speciation, and global distribution of this sentinel marine alga.
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Affiliation(s)
- Melinda P Simmons
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA Department of Ocean Sciences, University of California Santa Cruz
| | - Charles Bachy
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA
| | - Sebastian Sudek
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA
| | | | - Lisa Sudek
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA
| | - Manuel Ares
- Department of Molecular, Cell & Developmental Biology, University of California Santa Cruz
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA Department of Ocean Sciences, University of California Santa Cruz Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
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Worden AZ, Lee JH, Mock T, Rouzé P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, Foulon E, Grimwood J, Gundlach H, Henrissat B, Napoli C, McDonald SM, Parker MS, Rombauts S, Salamov A, Von Dassow P, Badger JH, Coutinho PM, Demir E, Dubchak I, Gentemann C, Eikrem W, Gready JE, John U, Lanier W, Lindquist EA, Lucas S, Mayer KFX, Moreau H, Not F, Otillar R, Panaud O, Pangilinan J, Paulsen I, Piegu B, Poliakov A, Robbens S, Schmutz J, Toulza E, Wyss T, Zelensky A, Zhou K, Armbrust EV, Bhattacharya D, Goodenough UW, Van de Peer Y, Grigoriev IV. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science 2009; 324:268-72. [PMID: 19359590 DOI: 10.1126/science.1167222] [Citation(s) in RCA: 416] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90% of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.
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Benitez-Nelson CR, Bidigare RR, Dickey TD, Landry MR, Leonard CL, Brown SL, Nencioli F, Rii YM, Maiti K, Becker JW, Bibby TS, Black W, Cai WJ, Carlson CA, Chen F, Kuwahara VS, Mahaffey C, McAndrew PM, Quay PD, Rappé MS, Selph KE, Simmons MP, Yang EJ. Mesoscale Eddies Drive Increased Silica Export in the Subtropical Pacific Ocean. Science 2007; 316:1017-21. [PMID: 17510362 DOI: 10.1126/science.1136221] [Citation(s) in RCA: 200] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Mesoscale eddies may play a critical role in ocean biogeochemistry by increasing nutrient supply, primary production, and efficiency of the biological pump, that is, the ratio of carbon export to primary production in otherwise nutrient-deficient waters. We examined a diatom bloom within a cold-core cyclonic eddy off Hawaii. Eddy primary production, community biomass, and size composition were markedly enhanced but had little effect on the carbon export ratio. Instead, the system functioned as a selective silica pump. Strong trophic coupling and inefficient organic export may be general characteristics of community perturbation responses in the warm waters of the Pacific Ocean.
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Affiliation(s)
- Claudia R Benitez-Nelson
- Department of Geological Sciences and Marine Science Program, University of South Carolina, Columbia, SC 29208, USA.
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Baumberger N, Doesseger B, Guyot R, Diet A, Parsons RL, Clark MA, Simmons MP, Bedinger P, Goff SA, Ringli C, Keller B. Whole-genome comparison of leucine-rich repeat extensins in Arabidopsis and rice. A conserved family of cell wall proteins form a vegetative and a reproductive clade. Plant Physiol 2003; 131:1313-26. [PMID: 12644681 PMCID: PMC166891 DOI: 10.1104/pp.102.014928] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2002] [Revised: 11/05/2002] [Accepted: 12/12/2002] [Indexed: 05/19/2023]
Abstract
We have searched the Arabidopsis and rice (Oryza sativa) genomes for homologs of LRX1, an Arabidopsis gene encoding a novel type of cell wall protein containing a leucine-rich repeat (LRR) and an extensin domain. Eleven and eight LRX (LRR/EXTENSIN) genes have been identified in these two plant species, respectively. The LRX gene family encodes proteins characterized by a short N-terminal domain, a domain with 10 LRRs, a cysteine-rich motif, and a variable C-terminal extensin-like domain. Phylogenetic analysis performed on the conserved domains indicates the existence of two major clades of LRX proteins that arose before the eudicot/monocot divergence and then diversified independently in each lineage. In Arabidopsis, gene expression studies by northern hybridization and promoter::uidA fusions showed that the two phylogenetic clades represent a specialization into "reproductive" and "vegetative" LRXs. The four Arabidopsis genes of the "reproductive" clade are specifically expressed in pollen, whereas the seven "vegetative" genes are predominantly expressed in various sporophytic tissues. This separation into two expression classes is also supported by previous studies on maize (Zea mays) and tomato (Lycopersicon esculentum) LRX homologs and by information on available rice ESTs. The strong conservation of the amino acids responsible for the putative recognition specificity of the LRR domain throughout the family suggests that the LRX proteins interact with similar ligands.
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Affiliation(s)
- Nicolas Baumberger
- Institute of Plant Biology, University of Zurich, CH-8008 Zurich, Switzerland
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Simmons MP, Savolainen V, Clevinger CC, Archer RH, Davis JI. Phylogeny of the Celastraceae inferred from 26S nuclear ribosomal DNA, phytochrome B, rbcL, atpB, and morphology. Mol Phylogenet Evol 2001; 19:353-66. [PMID: 11399146 DOI: 10.1006/mpev.2001.0937] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Phylogenetic relationships within Celastraceae (spindle-tree family) were inferred from nucleotide sequence characters from the 5' end of 26S nuclear ribosomal DNA (including expansion segments D1-D3; 84 species sampled), phytochrome B (58 species), rbcL (31 species), atpB (23 species), and morphology (94 species). Among taxa of questionable affinity, Forsellesia is a member of Crossosomataceae, and Goupia is excluded from Celastraceae. However, Brexia, Canotia, Lepuropetalon, Parnassia, Siphonodon, and Stackhousiaceae are supported as members of Celastraceae. Gymnosporia and Tricerma are distinct from Maytenus, Cassine is supported as distinct from Elaeodendron, and Dicarpellum is distinct from Salacia. Catha, Maytenus, and Pristimera are not resolved as natural genera. Hippocrateaceae (including Plagiopteron and Lophopetalum) are a clade nested within a paraphyletic Celastraceae. These data also suggest that the Loesener's classification of Celastraceae sensu stricto and Hallé's classification of Hippocrateaceae are artificial. The diversification of the fruit and aril within Celastraceae appears to be complex, with multiple origins of most fruit and aril forms.
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Affiliation(s)
- M P Simmons
- L. H. Bailey Hortorium, Cornell University, 462 Mann Library, Ithaca, New York 14853, USA
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Simmons MP, Ochoterena H, Carr TG. Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses. Syst Biol 2001; 50:454-62. [PMID: 12116587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Affiliation(s)
- M P Simmons
- L.H. Bailey Hortorium, 462 Mann Library, Cornell University, Ithaca, New York 14853, USA.
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Simmons MP, Clevinger CC, Savolainen V, Archer RH, Mathews S, Doyle JJ. Phylogeny of the Celastraceae inferred from phytochrome B gene sequence and morphology. Am J Bot 2001; 88:313-325. [PMID: 11222252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Phylogenetic relationships within Celastraceae were inferred using a simultaneous analysis of 61 morphological characters and 1123 base pairs of phytochrome B exon 1 from the nuclear genome. No gaps were inferred, and the gene tree topology suggests that the primers were specific to a single locus that did not duplicate among the lineages sampled. This region of phytochrome B was most useful for examining relationships among closely related genera. Fifty-one species from 38 genera of Celastraceae were sampled. The Celastraceae sensu lato (including Hippocrateaceae) were resolved as a monophyletic group. Loesener's subfamilies and tribes of Celastraceae were not supported. The Hippocrateaceae were resolved as a monophyletic group nested within a paraphyletic Celastraceae sensu stricto. Goupia was resolved as more closely related to Euphorbiaceae, Corynocarpaceae, and Linaceae than to Celastraceae. Plagiopteron (Flacourtiaceae) was resolved as the sister group of Hippocrateoideae. Brexia (Brexiaceae) was resolved as closely related to Elaeodendron and Pleurostylia. Canotia was resolved as the sister group of Acanthothamnus within Celastraceae. Perrottetia and Mortonia were resolved as the sister group of the rest of the Celastraceae. Siphonodon was resolved as a derived member of Celastraceae. Maytenus was resolved as three disparate groups, suggesting that this large genus needs to be recircumscribed.
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Affiliation(s)
- M P Simmons
- L.H. Bailey Hortorium, 462 Mann Library, Cornell University, Ithaca, New York 14853 USA
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Simmons MP, Ochoterena H. Gaps as characters in sequence-based phylogenetic analyses. Syst Biol 2000; 49:369-81. [PMID: 12118412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Affiliation(s)
- M P Simmons
- L.H. Bailey Hortorium, 462 Mann Library, Ithaca, New York 14853, USA.
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Abstract
In this paper, we propose a new method (uninode coding) for coding duplicate (paralogous) genes to infer species trees. Uninode coding incorporates data from duplicated and unduplicated gene copies in phylogenetic analyses of taxa. Uninode coding utilizes global parsimony through the inclusion of both duplicated and unduplicated gene copies, allows one to code all data sources from a taxon into a single terminal, and overcomes problems of character dependence among duplicated and unduplicated gene copies. We present an example of uninode coding using the phytochrome A and phytochrome C data from a study by Donoghue and Mathews.
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Affiliation(s)
- M P Simmons
- L.H. Bailey Hortorium, Cornell University, Ithaca, New York, USA
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Davis JI, Simmons MP, Stevenson DW, Wendel JF. Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences. Syst Biol 1998; 47:282-310. [PMID: 12064229 DOI: 10.1080/106351598260923] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
We examined three parallel data sets with respect to qualities relevant to phylogenetic analysis of 20 exemplar monocotyledons and related dicotyledons. The three data sets represent restriction-site variation in the inverted repeat region of the chloroplast genome, and nucleotide sequence variation in the chloroplast-encoded gene rbcL and in the mitochondrion-encoded gene atpA, the latter of which encodes the alpha-subunit of mitochondrial ATP synthase. The plant mitochondrial genome has been little used in plant systematics, in part because nucleotide sequence evolution in enzyme-encoding genes of this genome is relatively slow. The three data sets were examined in separate and combined analyses, with a focus on patterns of congruence, homoplasy, and data decisiveness. Data decisiveness (described by P. Goloboff) is a measure of robustness of support for most parsimonious trees by a data set in terms of the degree to which those trees are shorter than the average length of all possible trees. Because indecisive data sets require relatively fewer additional steps than decisive ones to be optimized on nonparsimonious trees, they will have a lesser tendency to be incongruent with other data sets. One consequence of this relationship between decisiveness and character incongruence is that if incongruence is used as a criterion of noncombinability, decisive data sets, which provide robust support for relationships, are more likely to be assessed as noncombinable with other data sets than are indecisive data sets, which provide weak support for relationships. For the sampling of taxa in this study, the atpA data set has about half as many cladistically informative nucleotides as the rbcL data set per site examined, and is less homoplastic and more decisive. The rbcL data set, which is the least decisive of the three, exhibits the lowest levels of character incongruence. Whatever the molecular evolutionary cause of this phenomenon, it seems likely that the poorer performance of rbcL than atpA, in terms of data decisiveness, is due to both its higher overall level of homoplasy and the fact that it is performing especially poorly at nonsynonymous sites.
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Affiliation(s)
- J I Davis
- L. H. Bailey Hortorium, Cornell University, Ithaca, New York 14853, USA
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Abstract
To investigate the effects of rubella on the performance of deaf subjects, a group of 30 rubella young deaf adults was compared to a group of 30 nonrubella young deaf adults on a series of measures that included the performance subtests of the WAIS, the Revised Beta, the Stanford Achievement Test, and the Utley Lipreading Test. For the 25 measures analyzed, the rubella-deaf group performed significantly poorer on the Digit Symbol subtest of both the WAIS and the Revised Beta, all subtests of the Stanford Achievement Test, and both subtests of the Utley Lipreading Test.
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Simmons MP. Is this maternity nursing? Nurs Outlook 1966; 14:66-8. [PMID: 5175443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Falk CR, Bucca HB, Simmons MP. A Comparative Study of the Use of Varying Concentrations of Agar in the Test Medium Used to Detect Contaminants in Biologic Products. J Bacteriol 1939; 37:121-31. [PMID: 16560193 PMCID: PMC374451 DOI: 10.1128/jb.37.2.121-131.1939] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- C R Falk
- Bureau of Laboratories of the Department of Health of the City of New York
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