### ### Challenges in Analysis and Interpretation of Microsatellite Data for Population Genetic Studies ### Putman, A.I. and I. Carbone ### Ecology and Evolution ### ### Supplemental Files and Procedure ### ### Note: directory and filenames need modification # Command scripts table_import.sh Shell script that creates article table, imports all records into table, and adds flag to denote journal groups cmd_1_script.mysql Run automatically by table_import.sh shell script. Creates MySQL table for article records cmd_2_script.mysql Run automatically by table_import.sh shell script. Compiles MySQL table for journals and adds flags to assign to one of four groups cmd_3_manual.mysql MySQL query for compiling article counts cmd_4_r.r R script for calculating percentages of total articles and arranging into table # Files created or edited manually jour_group_totals.csv Yearly article counts for the non-human, human, and PLoS One journal groups journal_human_not.csv Setting flag for journal as either human or non-human subject matter cmd_3_counts-output.csv Obtained by manually exporting grouped article counts using MySQL client paper_table.xlsx Added formatting for direct cut and paste into table ### ### Procedure ### ## ## 1. Download records in blocks of 500 (maximum allowed from WoS) ## -Place microsat and SNP records in separate folder 9/4/2014-9/5/14 WoS Core Collection ~2003-2014 (microsatellite OR SSR OR "simple sequence repeat" OR STR OR "simple tandem repeat" NOT (ISSR OR "inter simple sequence repeat")) Refined by: DOCUMENT TYPES: ( ARTICLE ) Timespan: All years. Indexes: SCI-EXPANDED. 9/5/2014-9/6/14 WoS Core Collection ~2003-2014 (snp or "single nucleotide polymorphism") Refined by: DOCUMENT TYPES: ( ARTICLE ) Timespan: All years. Indexes: SCI-EXPANDED. ## ## 2. Create, populate, and analyze database tables (table_import.sh shell script) ## -Export jour table to determine top journals and identify if human or non-human subject matter ## -export to journal_human_not.csv and upload into database to update field ## ## 3. Perform query to count records by group (non-human, human, minor journal), marker (microsatellite, SNP, both), and year ## -export to cmd_3_counts-output.csv ## -remove any quotes ## ## 4. Find total number of articles published for each year in the non-human group, PLoS One, and human journal group ## -make jour_group_totals.csv 9/10/14 WoS Core Collection Non-human journal group PUBLICATION NAME: ("BMC GENOMICS" OR "ZOOTAXA" OR "BMC EVOLUTIONARY BIOLOGY" OR "SCIENTIA HORTICULTURAE" OR "PLOS GENETICS" OR "INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES" OR "RUSSIAN JOURNAL OF GENETICS" OR "BIOCHEMICAL SYSTEMATICS AND ECOLOGY" OR "ECOLOGY AND EVOLUTION" OR "JOURNAL OF EVOLUTIONARY BIOLOGY" OR "MOLECULAR ECOLOGY" OR "PLANT BREEDING" OR "JOURNAL OF FISH BIOLOGY" OR "PLANT SYSTEMATICS AND EVOLUTION" OR "ANNALS OF BOTANY" OR "GENETIC RESOURCES AND CROP EVOLUTION" OR "GENETICA" OR "MODERN PATHOLOGY" OR "MOLECULAR BIOLOGY AND EVOLUTION" OR "NATURE GENETICS" OR "MOLECULAR BIOLOGY REPORTS" OR "THEORETICAL AND APPLIED GENETICS" OR "GENES & GENOMICS" OR "HEREDITY" OR "MOLECULAR BREEDING" OR "PHYTOPATHOLOGY" OR "TREE GENETICS & GENOMES" OR "BIOCHEMICAL GENETICS" OR "CONSERVATION GENETICS RESOURCES" OR "CONSERVATION GENETICS" OR "GENE" OR "EUPHYTICA" OR "INFECTION GENETICS AND EVOLUTION" OR "PLANT MOLECULAR BIOLOGY REPORTER" OR "ANIMAL GENETICS" OR "BMC PLANT BIOLOGY" OR "PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA" OR "AQUACULTURE" OR "BMC GENETICS" OR "PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES" OR "AMERICAN JOURNAL OF BOTANY" OR "CROP SCIENCE" OR "ELECTROPHORESIS" OR "ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES" OR "BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY" OR "MARINE BIOLOGY" OR "CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES" OR "JOURNAL OF HEREDITY" OR "MOLECULAR ECOLOGY RESOURCES" OR "GENETICS SELECTION EVOLUTION" OR "BIOINFORMATICS" OR "JOURNAL OF GENETICS" OR "NUCLEIC ACIDS RESEARCH" OR "JOURNAL OF ANIMAL SCIENCE" OR "EVOLUTION" OR "MOLECULAR PHYLOGENETICS AND EVOLUTION" OR "GENETIC TESTING AND MOLECULAR BIOMARKERS" OR "MAMMALIAN GENOME" OR "IMMUNOGENETICS" OR "TISSUE ANTIGENS" OR "GENOMICS" OR "BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS" OR "GENOME" OR "TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY" OR "GENOME RESEARCH" OR "JOURNAL OF THE AMERICAN SOCIETY FOR HORTICULTURAL SCIENCE" OR "MOLECULAR VISION" OR "JOURNAL OF DAIRY SCIENCE" OR "BREEDING SCIENCE" OR "GENETICS" OR "JOURNAL OF ANIMAL BREEDING AND GENETICS" OR "GENETICS AND MOLECULAR RESEARCH" OR "GENETICS AND MOLECULAR BIOLOGY" OR "MARINE ECOLOGY PROGRESS SERIES" OR "CLINICA CHIMICA ACTA" OR "MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS" OR "POULTRY SCIENCE" OR "GENES AND IMMUNITY" OR "AFRICAN JOURNAL OF BIOTECHNOLOGY" OR "NEUROSCIENCE LETTERS" OR "GENETIC EPIDEMIOLOGY" OR "MOLECULAR ECOLOGY NOTES" OR "BMC BIOINFORMATICS") AND YEAR PUBLISHED: (2004-2014) AND DOCUMENT TYPES: (Article) Timespan: All years. Indexes: SCI-EXPANDED. PLoS One PUBLICATION NAME: ("PLOS ONE") AND YEAR PUBLISHED: (2004-2014) AND DOCUMENT TYPES: (Article) Timespan: All years. Indexes: SCI-EXPANDED. Human journal group PUBLICATION NAME: ("JOURNAL OF CLINICAL MICROBIOLOGY" OR "AMERICAN JOURNAL OF SURGICAL PATHOLOGY" OR "CLINICAL CANCER RESEARCH" OR "ANTICANCER RESEARCH" OR "JOURNAL OF MEDICAL GENETICS" OR "BREAST CANCER RESEARCH AND TREATMENT" OR "HUMAN PATHOLOGY" OR "FAMILIAL CANCER" OR "CLINICAL GENETICS" OR "MALARIA JOURNAL" OR "BRITISH JOURNAL OF CANCER" OR "BMC CANCER" OR "ONCOGENE" OR "CHINESE MEDICAL JOURNAL" OR "INTERNATIONAL JOURNAL OF CANCER" OR "INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE" OR "ONCOLOGY REPORTS" OR "HUMAN MUTATION" OR "INTERNATIONAL JOURNAL OF LEGAL MEDICINE" OR "AMERICAN JOURNAL OF MEDICAL GENETICS PART A" OR "EUROPEAN JOURNAL OF HUMAN GENETICS" OR "HUMAN GENETICS" OR "JOURNAL OF FORENSIC SCIENCES" OR "FORENSIC SCIENCE INTERNATIONAL-GENETICS" OR "HUMAN IMMUNOLOGY" OR "WORLD JOURNAL OF GASTROENTEROLOGY" OR "HUMAN MOLECULAR GENETICS" OR "CARCINOGENESIS" OR "GASTROENTEROLOGY" OR "CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION" OR "CANCER RESEARCH" OR "JOURNAL OF CLINICAL ONCOLOGY" OR "PSYCHIATRIC GENETICS" OR "JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM" OR "GENES CHROMOSOMES & CANCER" OR "BLOOD" OR "INTERNATIONAL JOURNAL OF IMMUNOGENETICS" OR "FORENSIC SCIENCE INTERNATIONAL" OR "AMERICAN JOURNAL OF HUMAN GENETICS" OR "JOURNAL OF HUMAN GENETICS" OR "AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS" OR "HUMAN HEREDITY" OR "ASIAN PACIFIC JOURNAL OF CANCER PREVENTION" OR "PHARMACOGENOMICS JOURNAL" OR "ATHEROSCLEROSIS" OR "MOLECULAR PSYCHIATRY" OR "DIABETOLOGIA" OR "ANNALS OF HUMAN GENETICS" OR "BIOLOGICAL PSYCHIATRY" OR "DIABETES" OR "PHARMACOGENETICS AND GENOMICS" OR "CANCER GENETICS AND CYTOGENETICS" OR "PHARMACOGENOMICS" OR "JOURNAL OF RHEUMATOLOGY" OR "ANNALS OF THE RHEUMATIC DISEASES" OR "BMC MEDICAL GENETICS") AND YEAR PUBLISHED: (2004-2014) AND DOCUMENT TYPES: (Article) Timespan: All years. Indexes: SCI-EXPANDED. ## ## 5. Organize values into table and calculate percentages ## -run cmd_4_r.r script