Troublesome Science: The Misuse of Genetics and Genomics in Understanding Race

African population, 56; ancestors of, 63–64; blood groups of, 70–72, 72; emergence of Homo sapiens in, 19, 44–45; genome variation and, 163; in human genome phylogeny, 105–108, 106; mtDNA and, 77–79, 78; skin pigmentation in, 61–64; STRUCTURE algorithm and, 146–152, 147, 149–150; sub-Saharan, 109–111, 148; Y chromosomal lineages of, 80

Aguilera, Christina, 57

AIM. See ancestral informative marker

algorithms. See statistics

allelic frequencies, 10–11, 90, 137; adaptation conflation and, 165–167

allozyme analysis, 73–74, 137

“alt-right,” 175

amateur sport, 169–171, 188

American Indian, 58–59

Amerindian lineage, 116, 123, 124

Amos, William, 108, 183

ancestral informative marker (AIM), 91, 92, 125–126, 126, 138, 139; misrepresentation of, 163–164

Ancestral North Indian (ANI), 114

Ancestral South Indian (ASI), 114

ancestry company, 52

Angier, Natalie, 159

ANI. See Ancestral North Indian

Animalia (kingdom), 39

anthropologist, 17, 62, 96–97, 131, 173

ascertainment bias, 90–91, 125, 182

ascertainment process, 86–91, 89–90, 125–126, 146, 182

asexual gene transfer, 11

ASI. See Ancestral South Indian

Asian population: blood groups of, 70–72; genomic DNA and, 107; human migration and, 109–116, 113; skin pigmentation in, 63; STRUCTURE algorithm and, 146–152, 147, 149–150

Asiaticus, 23–24

athletics, 169–171, 188

autosome, 14, 83, 162

Bannon, Stephen K., 175

Bantu-speaking population, 111

Bar code of Life Database (BoLD), 47, 52, 180

barcoding gap, 54–55

base: of nucleotides, 13–14; of phylogenetic trees, 28

Bayesian statistics, 33–34, 99, 143

behaviorist, 130–131

Bering land bridge, 79

binominal nomenclature, 37–38

biological species concept, 19–20

“biology of race” controversy, 155–156

blood types, 69–73, 71–72, 181

Blumenbach, Johann Friedrich, 56

BoLD. See Bar code of Life Database

branching diagrams, 4–6, 5, 6. See also phylogenetic analysis

branching nodes, 25–26

Branta canadensis, 47

Breitbart News, 158–159

Brocchi, Giambattista, 3

Cambridge Reference Sample, 77

Caucasians, 56, 64, 163. See also European population

Caucasoid traits, 58

Cavalli-Sforza, Luca, 32, 70, 72, 73, 80, 137

CCES. See Cooperative Congressional Election Study

Chambers, John, C., 114

chimpanzee, 41, 104, 104, 124

chromosome painting, 145, 145

chromosomes, 14–15. See also deoxyribonucleic acid

classification terminology, 38–40, 39

clique analysis, 152

clustering methods: AIMS and, 91, 92, 125–126, 126, 138, 139, 163; dimension reduction in, 134–135, 135–136, 141–142; fineSTRUCTURE in, 144–145, 148, 151, 186; human populations and, 129–140, 130, 132, 134–135, 138; introduction to, xi; misunderstanding of, 162; model-based approach to, 142–144; pairwise distance in, 142; PCA in, 133–142, 134–135, 138, 145, 151, 185; STRUCTURE analysis, 143–153, 144–145, 147, 149–150

CNN. See Cable News Network

coalescent theory, 122–123

coancestry matrix, 145

CODIS. See Combined DNA Index System

COI. See cytochrome oxidase I gene

Colbert, Stephen, 162–165, 188

college athletics, 169–171, 188

Combined DNA Index System (CODIS), 47–52, 48–49, 180

compatibility analysis, 152

conservation biology, 19

Cooperative Congressional Election Study (CCES), 170, 174

Cope, Edward Drinker, 43–44

coverage, in sequencing, 86

cranial capacity, 60–61

crisis discipline, 19

cytochrome oxidase I gene (COI), 46–47

Darwin, Charles, 1–10, 6, 16, 57; maternal lineage of, 80, 82; notebooks on, 4, 5, 177–178; population thinking and, 18; statistics and, 129; Y chromosomal lineage of, 80, 82

data matrix, 31, 130

dendrogram, 132–133, 140–142

Denisova Cave, 88, 97

Denisovans, 79, 97, 99–101, 100, 102, 107–108

deoxyribonucleic acid (DNA), 31, 32–34, 107; barcoding of, x, 46–55, 48–49, 51, 53; CODIS and, 47–52, 48–49, 180; fingerprinting in, 46–55, 48–49, 51, 53; group inclusion in, 55; high-density chip sequencing and, 109, 110; introduction to, 12–15; microsatellite data and, 48–49, 49–52, 51, 180; microsatellite profiling and, 52, 74–80, 76, 78, 82; mtDNA and, 69–82, 71–72, 76, 78, 81; NGS in, 83–86; RFLP and, 74–75, 146; SNPs in, 83–91, 85, 89, 90, 92; STRUCTURE in, xi, 143–153, 144–145, 147, 149–150. See also phylogenetic analysis

DeSalle, Rob, ix, 45, 165, 177

Descent of Man, The (Darwin), 8–9, 57, 178

descent with modification, 2, 4

deutorostome, 39–40, 40

developmental system, 10

dichotomous branch, 120, 129

differentiation, 19–20

dimension reduction, 134–135, 135–136, 141–142

direct-to-consumer ancestry companies, 52

distance-based approach, 142–144

distance matrix, 141–142

diversification, 18, 77, 128

DNA. See deoxyribonucleic acid

domains, in taxonomy, 38–39

double helix, 13–14

Driver, H. E., 131, 185

Dunbar, Robin, 171, 188

EIGENSTRAT algorithm, 139, 185

endangered species, 19

Entertainment and Sports Programming Network (ESPN), 169

environmental pressure, 10, 109–110, 113, 167

Eriksson, Anders, 107–108, 183

ESPN. See Entertainment and Sports Programming Network

Essay on the Principle of Population, An (Malthus), 3, 178

Ethiopian population, 56

eugenics, ix, 80, 82, 129, 177

eukaryotes, 14, 38–39, 41

Eurasia, 112–114, 113, 184

Europaeus, 23–24

European gorse, 37–38

European population, 56, 91–93, 93, 182; skin pigmentation in, 61–64; STRUCTURE algorithm and, 146–152, 147, 149–150

evolutionary biology: Darwin and, 1–10, 5, 6, 16, 18; misunderstandings of, 162; of population, 6–7, 13–15; taxonomy in, 4–7, 5, 6, 27, 29; Wallace and, 1–3, 8. See also taxonomy

Evolutionary History of Man (Haeckel), 25, 26

false hypothesis, 155

family, in taxonomy, 2

Feather Identification Laboratory (FIL), 46–47

Fertile Crescent, 115

FIL. See Feather Identification Laboratory

fineSTRUCTURE, 144–145, 148, 151, 186

fossil evidence, 3, 26, 88; ancient genomes and, 95–98, 101, 102, 109; of early Homo sapiens, 57–59; in human migration, 109–114, 110, 113; of human remains, 96–99, 97, 99–100; microbial interactions and, 95–96

François, Oliver, 136, 185

Fungi (kingdom), 39, 41, 179

Galton, Francis, 82, 129–130, 130, 185

Garn, Stanley, 173, 188

gel electrophoresis, 49, 73

gender profiling, 52

genealogical tree, 75, 76

Genealogical World of Phylogenetic Networks, The (Morrison), 64, 180–181

genealogy: coalescent theory in, 122–123; single linkage group in, 121–123, 124; Woodger’s paradox in, 127–128

gene frequency, 16, 70, 90, 137; of microsatellites, 50–52, 51; in natural selection, 10–11

genes, introduction to, 13–14

Genetic Basis of Evolutionary Change, The (Lewontin), 73

genetic drift, 7–8, 16, 61

genomic study, xi; European population in, 91–93, 93, 182; paleogenomes in, 101, 109–116, 137, 183; PCA in, 133–142, 134–135, 138, 145, 151, 185; racialization of, 154–166, 177; visualization of, 130, 137; worldwide sampling summary of, 137–139, 138. See also phylogenetic analysis

genotype, 15, 63; of blood groups, 69–73, 71–72

“geographical races,” 126–127, 173

geographic clustering, 56, 91. See also migration

germ line mutation, 11

Ghiselin, Mike, 18–19

Gnathostomata, 40, 40

Gopalan, Prem, 148, 187

Gorilla (genus), 41

Gould, Stephen Jay, 8, 9, 59–60, 178, 180

Gower, J. C., 128, 151, 185

gravity, theory of, 8

Greenlee, Jill, 174–175, 189

Grooming, Gossip and the Evolution of Language (Dunbar), 188

groups, populations as, 17

hair, of mammals, 29

Hallwachs, Winnie, 47, 180

Hamilton, Andrew, 159, 188

Han population, 113–114

haplogroup, 75–82, 78, 81–82

haplotype: chromosome painting in, 145, 145; mtDNA phylogeny and, 75–80, 76, 78

Hawaiian Islands, 118, 132

Hebert, Paul, 46–47, 180

Hennig, Willi, 29–30, 126–127, 179

heterozygosity, 15, 118

HGDP. See Human Genome Diversity Project

high-density chip sequencing, 109, 110

Hirschfeld, Hanka, 69–70, 181

Hirschfeld, Ludwig, 69–70, 181

History and Geography of Human Genes, The (Cavalli-Sforza), 72, 73–74

HIV. See human immunodeficiency virus

Homo erectus, 77–79

Homo neanderthalensis, 19, 79, 108

Homo sapiens: branching within, 64–68, 65–67; early fossil records of, 57–59; emergence of, 19; geographic divisions within, 23–24; “geographic races” of, 126–127, 173; hierarchical classification of, 39–45, 40; language in, 36, 64, 65, 161, 172; migration patterns of, 109–119, 110, 113, 117; mtDNA phylogeny of, 97–104, 99–100, 103; Neolithic period and, 109–119, 110, 113, 117; Oceanian people and, 107, 112–113, 160; skull size in, 60–61; speciation of, 18–24, 20–22; whole-genome sequencing of, 102, 104, 109–114, 110, 145–148

Homo sapiens americanus, 44–45

Homo sapiens neanderthalensis, 38, 101

Homo sapiens sapiens, 38, 43, 45

Hooton, Earnest, 67, 67–68

human divergence, 7–8; ancient genomes and, 95–98, 101, 102, 109; branching within, 64–68, 65–67; coancestry matrix in, 145; early notions of, 56–68, 65–67; environmental pressure in, 10, 109–110, 113, 167; geographic groups in, 56, 67, 67–68; hypothesis testing and, 33, 55, 97, 155–158; language and, 64, 65; misrepresentation of, 154–167; phylogeography of, 120–128, 124, 126; population structure and, 111–114, 141–151, 187; Y chromosome haplogroups in, 80–82, 81–82. See also phylogenetic analysis

Human Genome Diversity Project (HGDP), 86, 97, 148

human immunodeficiency virus (HIV), 19

human populations: admixture in, 116–119, 138; AIMs in, 91–94, 92, 93; bottleneck in, 118; clustering methods and, 129–140, 130, 132, 134–135, 138; dichotomous branches in, 120, 129; inbreeding in, 118; Lewontin’s fallacy in, 151, 187; PCA in, 133–142, 134–135, 138, 145, 151, 185; reciprocal monophyly in, 120–125; serial founder effect in, 116–118, 117; STRUCTURE analysis of, xi, 143–153, 144–145, 147, 149–150. See also Homo sapiens

Human Races (Garn), 188

von Humboldt, Alexander, 37

hypothesis testing, 33, 55, 97, 155–158

ICZN. See International Code of Zoological Nomenclature

“impressionable years” hypothesis, 174–175

India, 14, 70, 87, 114, 161

Indiana Jones fallacy, 166

ingroup, 30, 31, 105

integrated taxonomy, 54, 180

interbreeding, 17–19, 105–109, 127–128, 143, 167

International Code of Zoological Nomenclature (ICZN), 38, 41, 43, 179

Janzen, Dan, 47, 180

Jewish population, 70, 137, 148

Jorde, Lynne, 151–152

journalist, xi, 36, 146, 156, 159

Keith, Sir Arthur, 64, 66

Kennewick Man, 58–59, 180

Kostenki paleogenome, 112, 113

Kroeber, A. L., 131, 185

Lamarck, Jean-Baptiste, 3, 25, 26, 179

Landsteiner, Karl, 69, 181

language: in stereotyping, 161, 172–173, 188; in taxonomic organization, 36, 64, 65, 161, 172

Lawson, Daniel, 144–145, 150, 186

lectotypes, 42–43, 44

length polymorphism, 49. See also restriction fragment length polymorphism

Lewis, Jason, 59–60

Lewontin, Richard, 8, 9, 73

Lewontin’s fallacy, 151, 187

Linnaean hierarchy, 38, 41–42

Linnaeus, Carolus, 21, 23–24, 37–38, 56

Liu, Jianjun, 113–114

Livingstone, Frank, 160

low coverage, 87–88, 98, 114

Malays (Indo-Pacific inhabitants), 56

Mal’ta-Buret paleogenome, 112, 113

Mal’ta lineage, 112, 113, 115–116

Malthus, Thomas, 3, 178

Mammalia, 17, 29, 37, 40, 40–41

Manica, Andrea, 107–108, 183

maternal inheritance, 74, 121, 162. See also mitochondrial deoxyribonucleic acid

maximum-likelihood approach, 27, 32–34; in blood groups, 70–72, 72

maximum parsimony, 27

Max Planck Institute, 96, 98

Mayr, Ernst, 4, 17–19, 178

Mayr species concept, 18

Measures of Taxonomic Distance and Their Analysis (Gower), 128, 151, 185

Michael, John, 59–60

microbe, 12, 15, 95–96

microbial deoxyribonucleic acid, 96, 98

“micro-races,” 173

microsatellite data, 48–49, 49–52, 51, 180; profiling and, 74–80, 76, 78, 82

middle east population, 114, 149, 161

migration: China in, 87, 112–114; Eurasia and, 112–114, 113, 184; fossil evidence in, 109–114, 110, 113; Hawaiian Islands in, 118, 132; of human populations, x–xi; patterns of, 109–119, 110, 113, 117; Polynesia in, 113, 116, 131, 132, 185; regionality and, 158; serial founder effect in, 116–118, 117

mitochondrial deoxyribonucleic acid (mtDNA): blood groups and, 69–73, 71–72; Darwin lineage of, 80, 82; genealogical tree of, 75, 76; microsatellite profiling and, 52, 74–80, 76, 78, 82; origin of Homo sapiens, 77–79, 78

mitochondrial Eve, x, 75, 181

model-based approach, to clustering, 142–144

molecular clock method, 34

Mongolian population, 56, 64

monophyletic group, 34, 54, 77; in blood groups, 70–72, 72; of Eukaryota, 39; reciprocal monophyly and, 120–125; in taxonomy, 120, 125–126

Monstrosus, 23–24

Morton, Samuel George, 59–60, 180

Mount Everest paradox, 164

mtDNA. See mitochondrial deoxyribonucleic acid

multicellularity, 12

multiethic society, 171–172

Murray, Charles, 154, 166, 188

Myth of Race, The: The Troubling Persistence of an Unscientific Idea (Sussman), ix, 177

National Geographic Society Genographic Project, 86

nationalism, 159–160

Native American, 58–59, 79, 113, 115–116

natural history, 1–10, 5, 6, 16, 18

natural selection, 15–16; branching diagrams and, 4–6, 5, 6; Darwin and, 3–4; populations and, 7–9

Natural Varieties of Humankind, On the (Blumenbach), 56

NCAA. See National College Athletic Association

Neanderthal, 38, 60, 63–64; ABBA/BABA test and, 104, 104–108, 106, 183; genes of, 19, 106, 108; mtDNA phlyogeny of, 97–104, 99–100, 103; Yoruba genome and, 87, 90, 104, 104–105, 106

Neolithic period, 109–119, 110, 113, 117

neutrality, in evolution, 7, 15–16

neutral variants, 16, 61

New Guinea, 112–113

Newton, Sir Isaac, 8

New York Times, 175

next-generation sequencing (NGS), 83–86

Nielsen, Rasmus, 110–111, 115, 184

nodes, in phylogeny, 27–28

nomenclature, 36–45, 39–40

Northeast Peru Indians, 131

Northwest Coast Indians, 131

nosce te ipsum, 23

Novembre, John, 91–94, 115, 144, 151, 182, 186–187

Nteta, Tatishe, 174–175, 188–189

nuclear membrane, 38

numerical taxonomy, 28

Numerical Taxonomy (Sokal and Sneath), 28, 131, 179

Obama, Barack, 37, 174–175, 189

Occidental Quarterly, 158, 188

Oceanian people, 107, 112–113, 160

“old-fashioned racism,” 174–175, 188–189

1KPG. See 1000 Genomes Project

O’Neal, Shaquille, 57

1000 Genomes Project (1KPG): paleogenomes in, 97, 101; phylogenetic analysis and, 122–125; SNPs in, 86, 87; STRUCTURE analysis of, 148, 150; Y chromosome analysis in, 80

On the Origin of Species by Means of Natural Selection; or, the Preservation of Favoured Races in the Struggle for Life (Darwin), 4–7, 6, 16, 25, 177–178

order, in phylogeny, 2

outgroup, 30–31, 31, 98, 104–105

outlier, in AIMs, 93

van Oven, Mannis, 77, 80

pairwise distance, 142

paleogenome, 101, 109–116, 137, 183

paleogenomic revolution, 101, 109

Paleoindian populations, 58

paleontologist, 17, 67–68

panmictic population, 7

parsimony, 27, 31–34, 32

paternal lineage, 80–82, 81–82

PCA. See principal components analysis

PCoA. See principal coordinates analysis

PCR. See polymerase chain reaction

Pearson, Karl, 129, 133

Pedigree of Man (Haeckel), 25, 26

Peter, Benjamin, 151, 187

phenetic method, 132

Philosophie Zoologique (Lamarck), 25, 26, 179

phylogenetic affinity, 28

phylogenetic analysis, 26–27; distance-based approach in, 142, 144; maximum parsimony in, 31–34, 32; misrepresentation of, 162; of mtDNA genomes, 98–104, 99–100, 103; of mtDNA haplotype, 75–80, 76, 78; PCoA in, 142; SNPs in, 83–91, 85, 89, 90, 92; STRUCTURE and, xi, 143–153, 144–145, 147, 149–150; unresolved trees in, 121–123, 162. See also statistics

Phylogenetic Systematics (Hennig), 29

phylogeography, 120–128, 124, 126

Pickrell, Joseph, 116, 118

pigmentation, of skin, 61–64

placental mammals, 41

Plantae (kingdom), 39

polymerase chain reaction (PCR), 49, 50

polymorphism, 16, 48–50; in blood groups, 70; RFLP in, 74–75, 146; SNPs in, 83–91, 85, 89, 90, 92

Polynesia, 113, 116, 131, 132, 185

Ponto-Caspian area, 115

population aggregation analysis, 53, 53

population genetics, 181; blood groups in, 70; Hennig in, 127–128; microsatellites in, 49–52, 51; PCA in, 133–142, 134–135, 138, 145, 151, 185; speciation of hominids in, 19–24, 20–22; STRUCTURE in, xi, 143–153, 144–145, 147, 149–150. See also phylogenetic analysis

population structure, 111–114, 141–150; Lewontin’s fallacy in, 151, 187

population thinking, 4, 7, 10, 18

Poznik, G. David, 80

Primer of Phylogenomics (DeSalle and Rosenfeld), 179

principal components analysis (PCA), 133–142, 134–135, 138, 145, 151, 185

principal coordinates analysis (PCoA), 142

Principles of Systematic Zoology (Mayr), 179

Pritchard, Jonathan, 141–146, 186

probability, 157; in microsatellite frequency, 50–52, 51; in natural selection, 7. See also statistics

progenitor species, 2

protein, introduction to, 12–14

Protista (kingdom), 39

de Queiroz, Kevin, 18, 178

race inferiority, 57

racial classification: ancestry conflation and, 164–165; attitudes in, 169–175; Homo sapiens taxonomy in, 38, 40, 43–45, 156; Indiana Jones fallacy and, 166; nationalism and, 159–160; regionality in, 158; subjectivity in, 156–158; taxonomic misrepresentation of, 158–162; variation conflation and, 165–167; white nationalism in, 158–159

Racimo, Fernando, 101, 109, 183–184

reciprocal monophyly, 120–125

recombination, 15, 83–84, 105, 122

recreational genomics, 165

regionality, in defining race, 158

Regnum Animalia (Linnaeus), 42

regression line, 129

Reich, David, 114, 118, 139

reproductive compatibility, 17–18

reproductive isolation, 17–18, 157

restriction fragment length polymorphism (RFLP), 74–75, 146

Rieppel, Olivier, 68

root, in phylogenetics, 28

Rosenberg, Noah, 146–148, 160–161, 186, 188

Rosenfeld, Jeff, 179, 184

sample size, 7; in AIM study, 93; in population speciation, 20–22, 20–24; in SNP analysis, 137; in STRUCTURE analysis, 146–148

self-centered world, 36

serial founder effect, 116–118, 117

sex chromosome, 14, 83

sex-limited genetic element, 83

Shintashta people, 113

short tandem repeat (STR), 49, 49, 52

Siberia, 88, 97, 113, 113, 115, 155

Sima de los Huesos, 96–104, 99–100, 103, 183

single linkage group, 121–123, 124

single nucleotide polymorphism (SNP), 83–91, 85, 89, 90, 92; in STRUCTURE analysis, 148–151, 149–150

skin pigmentation, 61–64, 180

Slatkin, Montgomery, 101, 109, 183–184

Smith, Samuel Stanhope, 2–3

Sneath, Peter, 28, 131–132

SNP. See single nucleotide polymorphism

social scientist, 130–131

Sokal, Robert, 28, 131–132

speciation, process of, 18

species, in taxonomy: concept of, 16–17; Darwin and, 2; Latin origin of, 16–17; molecular basis of, 12–24, 20–22

Statistical Inquiries into the Efficacy of Prayer (Galton), 129–130, 130, 185

statistics: AIMS and, 91, 92, 125–126, 126, 138, 139, 163; Bayesian statistics in, 33–34, 99, 143; clique analysis in, 152; compatibility analysis in, 152; EIGENSTRAT in, 139, 185; Galton and, 129–130, 130, 185; PCA in, 133–142, 134–135, 138, 145, 151, 185; population structure and, 111–114, 141–151, 187; regression line in, 129. See also clustering methods

Stearns, William, 43, 179

Stephen Colbert effect, 162–165, 188

Stephens, Matthew, 141, 185

Stewart, Patrick, 58

STR. See short tandem repeat

STRUCTURE analysis, xi, 143–153, 144–145, 147, 149–150, 186–187; misrepresentation and, 160–161

de St. Vincent, Jean-Baptiste Bory, 45

subjectivity, in racial classification, 156–158

sub-Saharan Africa, 109–111, 148

subspecies: differentiation and, 23; Homo sapiens and, 38, 40, 43–45, 156; misunderstanding of, 158–159; race as synonym for, 159

subspecific differentiation, 23

Sullenberger, Chesley, 46

Sussman, Robert, ix, 177

Systema Naturae (Linnaeus), 42

systematics, 27, 44, 56, 64; Hennig and, 29–30, 126–127, 179; phylogenetics and, 126–127, 131–132, 152, 162; taxonomy and, 22–23, 32, 39, 39, 54, 68

Tattersall, Ian, ix, 45, 165, 177

taxonomy, x; conclusions in speciation, 22–24; dendrograms in, 132–133, 140–142; domains in, 38–39; Hennig and, 29–30, 126–127, 179; language in, 36, 64, 65, 161, 172; maximum parsimony and, 31–34, 32; Mayr’s definitions of, 39, 39; misunderstandings of, 158–162; Numerical Taxonomy in, 28, 131, 179; phenetic methods in, 132. See also phylogenetic analysis