Horizontal gene transfer

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Horizontal_gene_transfer

Tree of life showing vertical and horizontal gene transfers

Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). HGT is an important factor in the evolution of many organisms. HGT is influencing scientific understanding of higher-order evolution while more significantly shifting perspectives on bacterial evolution.

Horizontal gene transfer is the primary mechanism for the spread of antibiotic resistance in bacteria, and plays an important role in the evolution of bacteria that can degrade novel compounds such as human-created pesticides and in the evolution, maintenance, and transmission of virulence. It often involves temperate bacteriophages and plasmids. Genes responsible for antibiotic resistance in one species of bacteria can be transferred to another species of bacteria through various mechanisms of HGT such as transformation, transduction and conjugation, subsequently arming the antibiotic resistant genes' recipient against antibiotics. The rapid spread of antibiotic resistance genes in this manner is becoming a challenge to manage in the field of medicine. Ecological factors may also play a role in the HGT of antibiotic resistant genes.

Horizontal gene transfer is recognized as a pervasive evolutionary process that distributes genes between divergent prokaryotic lineages and can also involve eukaryotes. HGT events are thought to occur less frequently in eukaryotes than in prokaryotes. However, growing evidence indicates that HGT is relatively common among many eukaryotic species and can have an impact on adaptation to novel environments. Its study, however, is hindered by the complexity of eukaryotic genomes and the abundance of repeat-rich regions, which complicate the accurate identification and characterization of transferred genes.

It is postulated that HGT promotes the maintenance of a universal life biochemistry and, subsequently, the universality of the genetic code.

History

Griffith's experiment, reported in 1928 by Frederick Griffith, was the first experiment suggesting that bacteria are capable of transferring genetic information through a process known as transformation. Griffith's findings were followed by research in the late 1930s and early 1940s that isolated DNA as the material that communicated this genetic information.

Horizontal genetic transfer was then described in Seattle in 1951, in a paper demonstrating that the transfer of a viral gene into Corynebacterium diphtheriae created a virulent strain from a non-virulent strain, simultaneously revealing the mechanism of diphtheria (that patients could be infected with the bacteria but not have any symptoms, and then suddenly convert later or never), and giving the first example for the relevance of the lysogenic cycle. Inter-bacterial gene transfer was first described in Japan in a 1959 publication that demonstrated the transfer of antibiotic resistance between different species of bacteria. In the mid-1980s, Syvanen postulated that biologically significant lateral gene transfer has existed since the beginning of life on Earth and has been involved in shaping all of evolutionary history.

As Jian, Rivera and Lake (1999) put it: "Increasingly, studies of genes and genomes are indicating that considerable horizontal transfer has occurred between prokaryotes" (see also Lake and Rivera, 2007). The phenomenon appears to have had some significance for unicellular eukaryotes as well. As Bapteste et al. (2005) observe, "additional evidence suggests that gene transfer might also be an important evolutionary mechanism in protist evolution."

Grafting of one plant to another can transfer chloroplasts (organelles in plant cells that conduct photosynthesis), mitochondrial DNA, and the entire cell nucleus containing the genome to potentially make a new species. Some Lepidoptera (e.g. monarch butterflies and silkworms) have been genetically modified by horizontal gene transfer from the wasp bracovirus. Bites from insects in the family Reduviidae (assassin bugs) can, via a parasite, infect humans with the trypanosomal Chagas disease, which can insert its DNA into the human genome. It has been suggested that lateral gene transfer to humans from bacteria may play a role in cancer.

Aaron Richardson and Jeffrey D. Palmer state: "Horizontal gene transfer (HGT) has played a major role in bacterial evolution and is fairly common in certain unicellular eukaryotes. However, the prevalence and importance of HGT in the evolution of multicellular eukaryotes remain unclear."

Due to the increasing amount of evidence suggesting the importance of these phenomena for evolution (see below) molecular biologists such as Peter Gogarten have described horizontal gene transfer as "A New Paradigm for Biology".

Mechanisms

There are several mechanisms for horizontal gene transfer:

• Transformation, the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material (DNA or RNA). This process is relatively common in bacteria, but less so in eukaryotes. Transformation is often used in laboratories to insert novel genes into bacteria for experiments or for industrial or medical applications. See also molecular biology and biotechnology.
• Transduction, the process in which bacterial DNA is moved from one bacterium to another by a virus (a bacteriophage, or phage).
• Bacterial conjugation, a process that involves the transfer of DNA via a plasmid from a donor cell to a recombinant recipient cell during cell-to-cell contact.
• Gene transfer agents, virus-like elements encoded by the host that are found in the alphaproteobacteria order Rhodobacterales.

Horizontal transposon transfer

A transposable element (TE) (also called a transposon or jumping gene) is a mobile segment of DNA that can sometimes pick up a resistance gene and insert it into a plasmid or chromosome, thereby inducing horizontal gene transfer of antibiotic resistance.

Horizontal transposon transfer (HTT) refers to the passage of pieces of DNA that are characterized by their ability to move from one locus to another between genomes by means other than parent-to-offspring inheritance. Horizontal gene transfer has long been thought to be crucial to prokaryotic evolution, but there is a growing amount of data showing that HTT is a common and widespread phenomenon in eukaryote evolution as well. On the transposable element side, spreading between genomes via horizontal transfer may be viewed as a strategy to escape purging due to purifying selection, mutational decay and/or host defense mechanisms.

HTT can occur with any type of transposable elements, but DNA transposons and LTR retroelements are more likely to be capable of HTT because both have a stable, double-stranded DNA intermediate that is thought to be sturdier than the single-stranded RNA intermediate of non-LTR retroelements, which can be highly degradable. Non-autonomous elements may be less likely to transfer horizontally compared to autonomous elements because they do not encode the proteins required for their own mobilization. The structure of these non-autonomous elements generally consists of an intronless gene encoding a transposase protein, and may or may not have a promoter sequence. Those that do not have promoter sequences encoded within the mobile region rely on adjacent host promoters for expression. Horizontal transfer is thought to play an important role in the TE life cycle. In plants, it appears that LTR retrotransposons of the Copia superfamilies, especially those with low copy numbers from the Ale and Ivana lineages, are more likely to undergo horizontal transfer between different plant species.

HTT has been shown to occur between species and across continents in both plants and animals (Ivancevic et al. 2013), though some TEs have been shown to more successfully colonize the genomes of certain species over others. Both spatial and taxonomic proximity of species has been proposed to favor HTTs in plants and animals. It is unknown how the density of a population may affect the rate of HTT events within a population, but close proximity due to parasitism and cross contamination due to crowding have been proposed to favor HTT in both plants and animals. In plants, the interaction between lianas and trees has been shown to facilitate HTT in natural ecosystems. Successful transfer of a transposable element requires delivery of DNA from donor to host cell (and to the germ line for multi-cellular organisms), followed by integration into the recipient host genome. Though the actual mechanism for the transportation of TEs from donor cells to host cells is unknown, it is established that naked DNA and RNA can circulate in bodily fluid. Many proposed vectors include arthropods, viruses, freshwater snails (Ivancevic et al. 2013), endosymbiotic bacteria, and intracellular parasitic bacteria. In some cases, even TEs facilitate transport for other TEs.

The arrival of a new TE in a host genome can have detrimental consequences because TE mobility may induce mutation. However, HTT can also be beneficial by introducing new genetic material into a genome and promoting the shuffling of genes and TE domains among hosts, which can be co-opted by the host genome to perform new functions. Moreover, transposition activity increases the TE copy number and generates chromosomal rearrangement hotspots. HTT detection is a difficult task because it is an ongoing phenomenon that is constantly changing in frequency of occurrence and composition of TEs inside host genomes. Furthermore, few species have been analyzed for HTT, making it difficult to establish patterns of HTT events between species. These issues can lead to the underestimation or overestimation of HTT events between ancestral and current eukaryotic species.

Methods of detection

A speciation event produces orthologs of a gene in the two daughter species. A horizontal gene transfer event from one species to another adds a xenolog of the gene to the receiving genome.

Main article: Inferring horizontal gene transfer

Horizontal gene transfer is typically inferred using bioinformatics methods, either by identifying atypical sequence signatures ("parametric" methods) or by identifying strong discrepancies between the evolutionary history of particular sequences compared to that of their hosts. The transferred gene (xenolog) found in the receiving species is more closely related to the genes of the donor species than would be expected.

Viruses

The virus called Mimivirus infects amoebae. Another virus, called Sputnik, also infects amoebae, but it cannot reproduce unless mimivirus has already infected the same cell.

Sputnik's genome reveals further insight into its biology. Although 13 of its genes show little similarity to any other known genes, three are closely related to mimivirus and mamavirus genes, perhaps cannibalized by the tiny virus as it packaged up particles sometime in its history. This suggests that the satellite virus could perform horizontal gene transfer between viruses, paralleling the way that bacteriophages ferry genes between bacteria.

Horizontal transfer is also seen between geminiviruses and tobacco plants.

Prokaryotes

Horizontal gene transfer is common among bacteria, even among very distantly related ones, and also between bacteria and archaea. This process is thought to be a significant cause of increased drug resistance when one bacterial cell acquires resistance, and the resistance genes are transferred to the other species. Transposition and horizontal gene transfer, along with strong natural selective forces have led to multi-drug resistant strains of S. aureus and many other pathogenic bacteria. Horizontal gene transfer also plays a role in the spread of virulence factors, such as exotoxins and exoenzymes, amongst bacteria. A prime example concerning the spread of exotoxins is the adaptive evolution of Shiga toxins in E. coli through horizontal gene transfer via transduction with Shigella species of bacteria. Strategies to combat certain bacterial infections by targeting these specific virulence factors and mobile genetic elements have been proposed. For example, horizontally transferred genetic elements play important roles in the virulence of E. coli, Salmonella, Streptococcus and Clostridium perfringens.

In prokaryotes, restriction-modification systems are known to provide immunity against horizontal gene transfer and in stabilizing mobile genetic elements. Genes encoding restriction modification systems have been reported to move between prokaryotic genomes within mobile genetic elements (MGE) such as plasmids, prophages, insertion sequences/transposons, integrative conjugative elements (ICE), and integrons. Still, they are more frequently a chromosomal-encoded barrier to MGE than an MGE-encoded tool for cell infection.

Lateral gene transfer via a mobile genetic element, namely the integrated conjugative element (ICE) Bs1 has been reported for its role in the global DNA damage SOS response of the gram positive Bacillus subtilis. Furthermore, it has been linked with the radiation and desiccation resistance of Bacillus pumilus SAFR-032 spores, isolated from spacecraft cleanroom facilities.

Transposon insertion elements have been reported to increase the fitness of gram-negative E. coli strains through either major transpositions or genome rearrangements, and increasing mutation rates. In a study on the effects of long-term exposure of simulated microgravity on non-pathogenic E. coli, the results showed transposon insertions occur at loci, linked to SOS stress response. When the same E. coli strain was exposed to a combination of simulated microgravity and trace (background) levels of (the broad spectrum) antibiotic (chloramphenicol), the results showed transposon-mediated rearrangements (TMRs), disrupting genes involved in bacterial adhesion, and deleting an entire segment of several genes involved with motility and chemotaxis. Both of these studies have implications for microbial growth, adaptation to and antibiotic resistance in real time space conditions.

Horizontal gene transfer is particularly active in bacterial genomes around the production of secondary or specialized metabolites. This is clearly exhibited within certain groups of bacteria including P. aeruginosa and actinomycetales, an order of Actinomycetota. Polyketide synthases (PKSs) and biosynthetic gene clusters provide modular organizations of associated genes making these bacteria well-adapted to acquire and discard helpful modular modifications via HGT. Certain areas of genes known as hotspots further increase the likelihood of horizontally transferred secondary metabolite-producing genes. The promiscuity of enzymes is a reoccurring theme in this particular theatre.

Bacterial transformation

1: Donor bacterium 2: Bacterium who will receive the gene 3: The red portion represents the gene that will be transferred. Transformation in bacteria happens in a certain environment.

Natural transformation is a bacterial adaptation for DNA transfer (HGT) that depends on the expression of numerous bacterial genes whose products are responsible for this process. In general, transformation is a complex, energy-requiring developmental process. In order for a bacterium to bind, take up and recombine exogenous DNA into its chromosome, it must become competent, that is, enter a special physiological state. Competence development in Bacillus subtilis requires expression of about 40 genes. The DNA integrated into the host chromosome is usually (but with infrequent exceptions) derived from another bacterium of the same species, and is thus homologous to the resident chromosome. The capacity for natural transformation occurs in at least 67 prokaryotic species. Competence for transformation is typically induced by high cell density and/or nutritional limitation, conditions associated with the stationary phase of bacterial growth. Competence appears to be an adaptation for DNA repair. Transformation in bacteria can be viewed as a primitive sexual process, since it involves interaction of homologous DNA from two individuals to form recombinant DNA that is passed on to succeeding generations. Although transduction is the form of HGT most commonly associated with bacteriophages, certain phages may also be able to promote transformation.

Bacterial conjugation

1: Donor bacterium cell (F+ cell) 2: Bacterium that receives the plasmid (F- cell) 3: Plasmid that will be moved to the other bacterium 4: Pilus and T4SS. Conjugation in bacteria using a sex pilus; then the bacterium that received the plasmid can go give it to other bacteria as well.

E. coli cells going through conjugation and sharing genetic information. F-pilus is reaching towards other cell.

As mentioned before, conjugation is a method of horizontal gene transfer through cell to cell contact. Through the process of conjugation, type IV Secretion Systems (T4SS) are used to passage on DNA from the donor cell to the recipient cell. These T4SS encoded within the plasmid carry other proteins and genes that help supplement the cell in conjugation. Research has shown that there are Single Binding DNA Binding proteins (SSBs) also encoded within the conjugative plasmid may help with conjugation and cell viability. This is thought to be the case because SSBs naturally are expressed to help with stabilizing single-stranded DNA (ssDNA). SSBs will also recruit other proteins like RadD or RecA expressed in events of DNA recombination, repair, and replication. Further showcasing their possible role in conjugation. Although it may help, studies have also shown for proteins like SSB to not be essential in conjugation. For example, the plasmid pCF10 from Enterococcus faecalis, a gram-positive bacterium, has a SSB like-protein called PrgE and was classified for not being required for conjugation. More work needs to be done on why proteins that bind to ssDNA are encoded into conjugative plasmids.

Conjugation in the case of microbiomes and symbioses is very important. From this process new genes are acquired that lead to increasing genetic diversity and evolution such as the acquisition of antibiotic resistance genes. Mycobacterium tuberculosis is a species that has evolved through methods like conjugation while gaining antibiotic resistance. This evolution or increase in genetic diversity is also seen in many other species. Due to this, there is a huge concern on how impactful conjugation or horizontal gene transfer can be on human health and your microbiome as pathogenic microbes can become more pathogenic. Studies have shown that even our own microbiome has a plethora of antimicrobial genes which if transferred to pathogenic microbes could be detrimental.

Conjugation in Mycobacterium smegmatis, like conjugation in E. coli, requires stable and extended contact between a donor and a recipient strain, is DNase resistant, and the transferred DNA is incorporated into the recipient chromosome by homologous recombination. However, unlike E. coli high frequency of recombination conjugation (Hfr), mycobacterial conjugation is a type of HGT that is chromosome rather than plasmid based. Furthermore, in contrast to E. coli (Hfr) conjugation, in M. smegmatis all regions of the chromosome are transferred with comparable efficiencies. Substantial blending of the parental genomes was found as a result of conjugation, and this blending was regarded as reminiscent of that seen in the meiotic products of sexual reproduction.

Archaeal DNA transfer

Haloarchaea are aerobic halophiles thought to have evolved from anaerobic methanogens. A large amount of their genome, 126 composite gene families, are derived from genetic material from bacterial genomes. This has allowed them to adapt to extremely salty environments.

The archaeon Sulfolobus solfataricus, when UV irradiated, strongly induces the formation of type IV pili which then facilitates cellular aggregation. Exposure to chemical agents that cause DNA damage also induces cellular aggregation. Other physical stressors, such as temperature shift or pH, do not induce aggregation, suggesting that DNA damage is a specific inducer of cellular aggregation.

UV-induced cellular aggregation mediates intercellular chromosomal HGT marker exchange with high frequency, and UV-induced cultures display recombination rates that exceed those of uninduced cultures by as much as three orders of magnitude. S. solfataricus cells aggregate preferentially with other cells of their own species. Frols et al. and Ajon et al. suggested that UV-inducible DNA transfer is likely an important mechanism for providing increased repair of damaged DNA via homologous recombination. This process can be regarded as a simple form of sexual interaction.

Another thermophilic species, Sulfolobus acidocaldarius, is able to undergo HGT. S. acidocaldarius can exchange and recombine chromosomal markers at temperatures up to 84 °C. UV exposure induces pili formation and cellular aggregation. Cells with the ability to aggregate have greater survival than mutants lacking pili that are unable to aggregate. The frequency of recombination is increased by DNA damage induced by UV-irradiation and by DNA damaging chemicals.

The ups operon, containing five genes, is highly induced by UV irradiation. The proteins encoded by the ups operon are employed in UV-induced pili assembly and cellular aggregation leading to intercellular DNA exchange and homologous recombination. Since this system increases the fitness of S. acidocaldarius cells after UV exposure, Wolferen et al. considered that transfer of DNA likely takes place in order to repair UV-induced DNA damages by homologous recombination.

Eukaryotes

"Sequence comparisons suggest recent horizontal transfer of many genes among diverse species including across the boundaries of phylogenetic 'domains'. Thus determining the phylogenetic history of a species can not be done conclusively by determining evolutionary trees for single genes."

Organelle to nuclear genome

• Analysis of DNA sequences suggests that horizontal gene transfer has occurred within eukaryotes from the chloroplast and mitochondrial genomes to the nuclear genome. As stated in the endosymbiotic theory, chloroplasts and mitochondria probably originated as bacterial endosymbionts of a progenitor to the eukaryotic cell.

Organelle to organelle

• Mitochondrial genes moved to parasites of the Rafflesiaceae plant family from their hosts and from chloroplasts of a still-unidentified plant to the mitochondria of the bean Phaseolus.

Bacteria to fungi

• Horizontal transfer occurs from bacteria to some fungi, such as the yeast Saccharomyces cerevisiae.

Bacteria to plants

• Agrobacterium, a pathogenic bacterium that causes cells to proliferate as crown galls and proliferating roots is an example of a bacterium that can transfer genes to plants and this plays an important role in plant evolution.
• Land plants and their close relatives, the charophycean green algae, share a set of glycosyl hydrolases. These enzymes were likely transferred from bacteria and fungi to the last common ancestor of these organisms before the origin of land plants.

Bacteria to animals

• HhMAN1 is a gene in the genome of the coffee berry borer (Hypothenemus hampei) that resembles bacterial genes, and is thought to be transferred from bacteria in the beetle's gut.
• oskar is an essential gene for the specification of the germline in Holometabola and its origin is through to be due to a HGT event followed by a fusion with a LOTUS domain.
• Bdelloid rotifers currently hold the 'record' for HGT in animals with ~8% of their genes from bacterial origins. Tardigrades were thought to break the record with 17.5% HGT, but that finding was an artifact of bacterial contamination.
• A study found the genomes of 40 animals (including 10 primates, four Caenorhabditis worms, and 12 Drosophila insects) contained genes which the researchers concluded had been transferred from bacteria and fungi by horizontal gene transfer. The researchers estimated that for some nematodes and Drosophila insects these genes had been acquired relatively recently.
• A bacteriophage-mediated mechanism transfers genes between prokaryotes and eukaryotes. Nuclear localization signals in bacteriophage terminal proteins (TP) prime DNA replication and become covalently linked to the viral genome. The role of virus and bacteriophages in HGT in bacteria, suggests that TP-containing genomes could be a vehicle of inter-kingdom genetic information transference all throughout evolution.
• The adzuki bean beetle has acquired genetic material from its (non-beneficial) endosymbiont Wolbachia. New examples have recently been reported demonstrating that Wolbachia bacteria represent an important potential source of genetic material in arthropods and filarial nematodes.
• The psyllid Pachypsylla venusta has acquired genes from its current endosymbiont Carsonella, and from many of its historical endosymbionts, too.

Plant to plant

• Striga hermonthica, a parasitic eudicot, has received a gene from sorghum (Sorghum bicolor) to its nuclear genome. The gene's functionality is unknown.
• A gene that allowed ferns to survive in dark forests came from the hornwort, which grows in mats on streambanks or trees. The neochrome gene arrived about 180 million years ago.
• Transfer of mRNA between host plants and heterotrophs plants in the Orobanchaceae have been directly observed. mRNA transcripts can therefore be a factor involved in the transfer and integration of foreign DNA in heterotrophs.

Plants to animals

• The eastern emerald sea slug Elysia chlorotica has been suggested by fluorescence in situ hybridization (FISH) analysis to contain photosynthesis-supporting genes obtained from an alga (Vaucheria litorea) in their diet. LGT in Sacoglossa is now thought to be an artifact and no trace of LGT was found upon sequencing the genome of Elysia chlorotica.
• The whitefly Bemisia tabaci acquired a plant detoxification gene that neutralizes plant toxins.

Plant to fungus

Main article: Plant-fungus horizontal gene transfer

• Gene transfer between plants and fungi has been posited for a number of cases, including rice (Oryza sativa).
• Evidence of gene transfer from plants was documented in the fungus Colletotrichum.
• Plant expansin genes were transferred to fungi further enabling the fungi to infect plants.

Plant to bacteria

• Plant expansin genes were transferred to bacteria further enabling the bacteria to infect plants.

Fungi to insects

• Pea aphids (Acyrthosiphon pisum) contain multiple genes from fungi. Plants, fungi, and microorganisms can synthesize carotenoids, but torulene made by pea aphids is the only carotenoid known to be synthesized by an organism in the animal kingdom.

Fungi to fungi

• The toxin α-amanitin is found in numerous, seemingly unrelated genera fungi such as Amanita, Lepiota, and Galerina. Two biosynthetic genes involved in the production of α-amanitin are P450-29 and FMO1. Phylogenetic and genetic analyses of these genes strongly indicate that they were transferred between the genera via horizontal gene transfer.
• The ToxA protein (wheat virulence protein) included in a ~14 kb element, containing both coding and non-coding regions was transferred between different fungal wheat patogens: Parastagonospora nodorum, Pyrenophora tritici-repentis, and Bipolaris sorokiniana.
• A large genomic element named "Wallaby," approximately 500 kb in length, was recently transferred between two Penicillium species used in cheesemaking: P. camemberti and P. roqueforti. Wallaby contains around 250 genes, including several that are thought to play a role in microbial competition.

Fungi to oomycetes

• 4 genes from Magnaporthe grisea, the rice blast fungus, were suspected to be horizontally transferred from the genus Phytophthora, and hypothesized to play a role in the fungus evolution into a plant pathogen.

Oomycetes to fungi

• The oomycete species Phytophthora ramorum, Phytophthora sojae, Phytophthora infestans, and Hyaloperonospora parasitica were estimated to have 33 horizontal gene transfers from fungi. The transferred genes were hypothesized to be involved in functions that facilitate plant tissues colonization, such as secreted proteins to evade plant immune response and breaking down plant cell walls.

Animals to animals

• Smelt fish received antifreeze protein (AFP) gene from herring through a direct horizontal transfer.

Animals to bacteria

• The strikingly fish-like copper/zinc superoxide dismutase of Photobacterium leiognathi is most easily explained in terms of transfer of a gene from an ancestor of its fish host.

Human to protozoan

• The malaria pathogen Plasmodium vivax acquired genetic material from humans that might help facilitate its long stay in the body.

Human genome

• One study identified approximately 100 of humans' approximately 20,000 total genes which likely resulted from horizontal gene transfer, but this number has been challenged by several researchers arguing these candidate genes for HGT are more likely the result of gene loss combined with differences in the rate of evolution.

Compounds found to promote horizontal gene transfer

Through research into the growing issue of antibiotic resistance certain compounds have been observed to promote horizontal gene transfer. Antibiotics given to bacteria at non-lethal levels have been known to be a cause of antibiotic resistance but emerging research is now showing that certain non-antibiotic pharmaceuticals (ibuprofen, naproxen, gemfibrozil, diclofenac, propranolol, etc.) also have a role in promoting antibiotic resistance through their ability to promote horizontal gene transfer (HGT) of genes responsible for antibiotic resistance. The transfer of antibiotic resistance genes (ARGs) through conjugation is significantly accelerated when donor cells with plasmids and recipient cells are introduced to each other in the presence of one of the pharmaceuticals. Non-antibiotic pharmaceuticals were also found to cause some responses in bacteria similar to those responses to antibiotics, such as increasing expression of the genes lexA, umuC, umuD and soxR involved in the bacteria's SOS response as well as other genes also expressed during exposure to antibiotics. These findings are from 2021 and due to the widespread use of non-antibiotic pharmaceuticals, more research needs to be done in order to further understanding on the issue.

Alongside non-antibiotic pharmaceuticals, other compounds relevant to antibiotic resistance have been tested such as malachite green, ethylbenzene, styrene, 2,4-dichloroaniline, trioxymethylene, o-xylene solutions, p-nitrophenol (PNP), p-aminophenol (PAP), and phenol (PhOH). It is a global concern that ARGs have been found in wastewater treatment plants Textile wastewater has been found to contain 3- to 13-fold higher abundance of mobile genetic elements than other samples of wastewater. The cause of this is the organic compounds used for textile dying (o-xylene, ethylbenzene, trioxymethylene, styrene, 2,4-dichloroaniline, and malachite green) raising the frequency of conjugative transfer when bacteria and plasmid (with donor) are introduced in the presence of these molecules. When textile wastewater combines with wastewater from domestic sewage, the ARGs present in wastewater are transferred at a higher rate due to the addition of textile dyeing compounds increasing the occurrence of HGT.

Other organic pollutants commonly found in wastewater have been the subject of similar experiments. A 2021 study used similar methods of using plasmid in a donor and mixing that with a receptor in the presence of compound in order to test horizontal gene transfer of antibiotic resistance genes but this time in the presence of phenolic compounds. Phenolic compounds are commonly found in wastewater and have been found to change functions and structures of the microbial communities during the wastewater treatment process. Additionally, HGT increases in frequency in the presence of the compounds p-nitrophenol (PNP), p-aminophenol (PAP), and phenol. These compounds result in a 2- to 9-fold increase in HGT (p-nitrophenol being on the lower side of 2-fold increases and p-aminophenol and phenol having a maximum increase of 9-fold). This increase in HGT is on average less than the compounds ibuprofen, naproxen, gemfibrozil, diclofenac, propranolol, o-xylene, ethylbenzene, trioxymethylene, styrene, 2,4-dichloroaniline, and malachite green but their increases is still significant. The study that came to this conclusion is similar to the study on horizontal gene transfer and non-antibiotic pharmaceuticals in that it was done in 2021 and leaves room for more research, specifically in the focus of the study which is activated sludge.

Heavy metals have also been found to promote conjugative transfer of antibiotic resistance genes. The paper that led to the discovery of this was done in 2017 during the emerging field of horizontal gene transfer assisting compound research. Metals assist in the spread of antibiotic resistance through both co-resistance as well as cross-resistance mechanisms. In quantities relevant to the environment, Cu(II), Ag(I), Cr(VI), and Zn(II) promote HGT from donor and receptor strains of E. coli. The presence of these metals triggered SOS response from bacterial cells and made the cells more permeable. These are the mechanisms that make even low levels of heavy metal pollution in the environment impact HGT and therefore the spread of ARGs.

Promiscuous DNA

Promiscuous DNA is a form of horizontal gene transfer that transmits genetic information across organellar barriers. Promiscuous DNA transfer has substantial evidence in its movement across the genome of numerous organisms, from movements in chloroplast to the nucleus, chloroplast to the mitochondria, and mitochondria to the nucleus.

History

In 1982, R. John Ellis defined this type of transpositional transfer mutation as "intracellular promiscuity". Ellis further explored the phenomenon of "intracellular promiscuity" through the experiments of David Stern and David Lonsdale, in which genetic transfer between chloroplasts to mitochondria was discovered, aiding in the definition and discovery of promiscuous DNA.

Mechanism

While much remains to be understood about how promiscuous DNA undergoes movement and transfer, numerous experiments have pointed to plastid sequences, ptDNA, as a key player. Plasmids, with their mobile nature and crucial role in horizontal gene transfer, are seen as a significant element in DNA that exchanges genetic information. This mobility makes ptDNA a potential donor for promiscuous DNA to traverse organellar barriers.

Types

NUMTs

NUMTs (nuclear sequences of mitochondrial) are a type of promiscuous DNA that arises from the natural transfer of mitochondria DNA (mtDNA) to the nuclear genome (nDNA). These NUMTs, with their varying frequencies, sizes, and features, contribute to the genetic diversity across all eukaryotes and, in some cases, to diseases among humans.

NUPTs

NUPTs (nuclear plastid DNA sequences) are a type of promiscuous DNA that arises from the natural transfer of ptDNA (plastid DNA) into nDNA. These fragments of ptDNA, similar to NUMTs in frequency, size, and features, also exhibit variability across species.

Artificial horizontal gene transfer

See also: Gene therapy

Before it is transformed, a bacterium is susceptible to antibiotics. A plasmid can be inserted when the bacteria is under stress, and be incorporated into the bacterial DNA creating antibiotic resistance. When the plasmids are prepared they are inserted into the bacterial cell by either making pores in the plasma membrane with temperature extremes and chemical treatments, or making it semi permeable through the process of electrophoresis, in which electric currents create the holes in the membrane. After conditions return to normal the holes in the membrane close and the plasmids are trapped inside the bacteria where they become part of the genetic material and their genes are expressed by the bacteria.

Genetic engineering is essentially horizontal gene transfer, albeit with synthetic expression cassettes. The Sleeping Beauty transposon system (SB) was developed as a synthetic gene transfer agent that was based on the known abilities of Tc1/mariner transposons to invade genomes of extremely diverse species. The SB system has been used to introduce genetic sequences into a wide variety of animal genomes.

In evolution

Main article: Horizontal gene transfer in evolution

Horizontal gene transfer is a potential confounding factor in inferring phylogenetic trees based on the sequence of one gene. For example, given two distantly related bacteria that have exchanged a gene a phylogenetic tree including those species will show them to be closely related because that gene is the same even though most other genes are dissimilar. For this reason, it is often ideal to use other information to infer robust phylogenies such as the presence or absence of genes or, more commonly, to include as wide a range of genes for phylogenetic analysis as possible.

For example, the most common gene to be used for constructing phylogenetic relationships in prokaryotes is the 16S ribosomal RNA gene since its sequences tend to be conserved among members with close phylogenetic distances, but variable enough that differences can be measured. However, in recent years it has also been argued that 16s rRNA genes can also be horizontally transferred. Although this may be infrequent, the validity of 16s rRNA-constructed phylogenetic trees must be reevaluated.

Biologist Johann Peter Gogarten suggests "the original metaphor of a tree no longer fits the data from recent genome research" therefore "biologists should use the metaphor of a mosaic to describe the different histories combined in individual genomes and use the metaphor of a net to visualize the rich exchange and cooperative effects of HGT among microbes". There exist several methods to infer such phylogenetic networks.

Using single genes as phylogenetic markers, it is difficult to trace organismal phylogeny in the presence of horizontal gene transfer. Combining the simple coalescence model of cladogenesis with rare HGT horizontal gene transfer events suggest there was no single most recent common ancestor that contained all of the genes ancestral to those shared among the three domains of life. Each contemporary molecule has its own history and traces back to an individual molecule cenancestor. However, these molecular ancestors were likely to be present in different organisms at different times."

Challenge to the tree of life

Further information: Last universal common ancestor and tree of life (biology)

Horizontal gene transfer poses a possible challenge to the concept of the last universal common ancestor (LUCA) at the root of the tree of life that was first formulated by Carl Woese, which led him to propose the Archaea as a third domain of life. Indeed, it was while examining the new three-domain model of life that horizontal gene transfer arose as a complicating issue: Archaeoglobus fulgidus was seen as an anomaly with respect to a phylogenetic tree, based upon the encoding for the enzyme HMGCoA reductase; the organism in question is a definite Archaean, with all the cell lipids and transcription machinery that are expected of an Archaean, but whose HMGCoA genes are of bacterial origin. Scientists are broadly agreed on symbiogenesis, that mitochondria in eukaryotes derived from alpha-proteobacterial cells and that chloroplasts came from ingested cyanobacteria, and other gene transfers may have affected early eukaryotes. (In contrast, multicellular eukaryotes have mechanisms to prevent horizontal gene transfer, including separated germ cells.) If there had been continued and extensive gene transfer, there would be a complex network with many ancestors, instead of a tree of life with sharply delineated lineages leading back to a LUCA. However, a LUCA can be identified, so horizontal transfers must have been relatively limited.

Other early HGTs are thought to have happened. The first common ancestor (FUCA), earliest ancestor of LUCA, had other descendants that had their own lineages. These now-extinct sister lineages of LUCA descending from FUCA are thought to have horizontally transferred some of their genes into the genome of early descendants of LUCA.

Phylogenetic information in HGT

It has been remarked that, despite the complications, the detection of horizontal gene transfers brings valuable phylogenetic and dating information.

The potential of HGT to be used for dating phylogenies has recently been confirmed.

The chromosomal organization of horizontal gene transfer

The acquisition of new genes has the potential to disorganize the other genetic elements and hinder the function of the bacterial cell, thus affecting the competitiveness of bacteria. Consequently, bacterial adaptation lies in a conflict between the advantages of acquiring beneficial genes, and the need to maintain the organization of the rest of its genome. Horizontally transferred genes are typically concentrated in only ~1% of the chromosome (in regions called hotspots). This concentration increases with genome size and with the rate of transfer. Hotspots diversify by rapid gene turnover; their chromosomal distribution depends on local contexts (neighboring core genes), and content in mobile genetic elements. Hotspots concentrate most changes in gene repertoires, reduce the trade-off between genome diversification and organization, and should be treasure troves of strain-specific adaptive genes. Most mobile genetic elements and antibiotic resistance genes are in hotspots, but many hotspots lack recognizable mobile genetic elements and exhibit frequent homologous recombination at flanking core genes. Overrepresentation of hotspots with fewer mobile genetic elements in naturally transformable bacteria suggests that homologous recombination and horizontal gene transfer are tightly linked in genome evolution.

Genes

There is evidence for historical horizontal transfer of the following genes:

• Lycopene cyclase for carotenoid biosynthesis, between Chlorobiota and "Cyanobacteria".
• TetO gene conferring resistance to tetracycline, between Campylobacter jejuni.
• Neochrome, a gene in some ferns that enhances their ability to survive in dim light. Believed to have been acquired from algae sometime during the Cretaceous.
• Transfer of a cysteine synthase from a bacterium into phytophagous mites and Lepidoptera allowing the detoxification of cyanogenic glucosides produced by host plants.
• The LINE1 sequence has transferred from humans to the gonorrhea bacteria.

Black genocide in the United States

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Black_genocide_in_the_United_States 

Paul Robeson signed the We Charge Genocide petition.

In the United States, black genocide is a historiographical framework and rhetorical term used to analyze the past and present impact of systemic racism on African Americans by both the United States government and white Americans. The decades of lynchings and long-term racial discrimination were first formally described as genocide by a now-defunct organization, the Civil Rights Congress, in a petition which it submitted to the United Nations in 1951. In the 1960s, Malcolm X accused the US government of engaging in human rights abuses, including genocide, against black people, citing long-term injustice, cruelty, and violence against blacks by whites.

The black genocide analogy has historically been applied to the war on drugs, war on crime, and war on poverty for their detrimental effects on the black community. During the Vietnam War, the increasing use of black soldiers was criticized as an expression of black genocide. In recent decades, the disproportionately high black prison population has also been described as black genocide.

Critics of the black genocide framework describe it as a conspiracy theory, while its proponents argue it is a useful framework for analyzing systemic racism. Arguments against birth control, in particular, have been criticized as conspiratorial or exaggerated, although attempts at black population control and government-sponsored compulsory sterilization did occur as recently as the 20th century.

Slavery as genocide

See also: Maafa

Slavery in general and the Atlantic slave trade in particular was an archetypal example of a crime against humanity in the 19th century, a larger category of crimes that was expanded when genocide was included in it in the 20th century. George Washington Williams popularized the concept of crimes against humanity with regard to the history of slavery in the United States and during the Congo Free State propaganda war of the 1890s, the "laws of humanity" were included in the Martens Clause of the Hague Conventions and as a result, they were legally enshrined in international law.

Canadian scholar Adam Jones characterizes the mass death of millions of Africans during the Atlantic slave trade as a genocide, calling it "one of the worst holocausts in human history" due to the fact that it resulted in 15 to 20 million deaths according to one estimate, and he has also stated that arguments to the contrary, such as the argument that "it was in slave owners' interest to keep slaves alive, not exterminate them", is "mostly sophistry" since "the killing and destruction were intentional, whatever the incentives to preserve survivors of the Atlantic passage for labor exploitation. To revisit the issue of intent already touched on: If an institution is deliberately maintained and expanded by discernible agents, though all are aware of the hecatombs of casualties it is inflicting on a definable human group, then why should this not qualify as genocide?"

In his book, The Broken Heart of America, Harvard professor Walter Johnson wrote that on many occasions throughout the history of the enslavement of Africans in the US, many instances of genocide occurred, instances which included the separation of men from their wives, effectively reducing the size of the African-American population. For a black American who lived during the era of U.S. slavery, no rights were guaranteed, whether they were personally enslaved or not. In the United States a slave's life expectancy was 21 to 22 years, and a black child through the age of 1 to 14 had twice the risk of dying of a white child of the same age.

Jim Crow as genocide

This image demonstrates segregation laws in practice in the Jim Crow era.

Petition to the United Nations

Main article: We Charge Genocide

The United Nations (UN) was formed in 1945. The UN debated and adopted a Genocide Convention in late 1948, holding that genocide was the "intent to destroy, in whole or in part", a racial group. Based on the "in part" definition, the Civil Rights Congress (CRC), a group composed of African Americans with Communist affiliations, presented to the UN in 1951 a petition called "We Charge Genocide." The petition listed 10,000 unjust deaths of African Americans in the nine decades since the American Civil War. It described lynching, mistreatment, murder and oppression by whites against blacks, concluding that the US government was refusing to address "the persistent, widespread, institutionalized commission of the crime of genocide". The petition was presented to the UN convention in Paris by CRC leader William L. Patterson, and in New York City by the singer and actor Paul Robeson who was a civil rights activist and a Communist member of CRC.

The Cold War raised American concerns about Communist expansionism. The CRC petition was viewed by the US government as being against America's best interests with regard to fighting Communism. The petition was ignored by the UN; many of the charter countries looked to the US for guidance and were not willing to arm the enemies of the US with more propaganda about its failures in domestic racial policy. American responses to the petition were various: Radio journalist Drew Pearson spoke out against the supposed "Communist propaganda" before it was presented to the UN.

Professor Raphael Lemkin, a Polish lawyer who had helped draft the UN Genocide Convention, said that the CRC petition was a misguided effort which drew attention away from the Soviet Union's genocide of Estonians, Latvians and Lithuanians. The National Association for the Advancement of Colored People (NAACP) issued a statement saying that there was no black genocide even though serious matters of racial discrimination certainly did exist in America. Walter Francis White, leader of the NAACP, wrote that the CRC petition contained "authentic" instances of discrimination, mostly taken from reliable sources. He said, "Whatever the sins of the nation against the Negro—and they are many and gruesome—genocide is not among them." UN Delegate Eleanor Roosevelt said that it was "ridiculous" to characterize long term discrimination as genocide.

The "We Charge Genocide" petition received more notice in international news than in domestic US media. French and Czech media carried the story prominently, as did newspapers in India. In 1952, African-American author J. Saunders Redding traveling in India was repeatedly asked questions about specific instances of civil rights abuse in the US, and the CRC petition was used by Indians to rebut his assertions that US race relations were improving. In the US, the petition faded from public awareness by the late 1950s. In 1964, Malcolm X and his Organization of Afro-American Unity, citing the same lynchings and oppression described in the CRC petition, began to prepare their own petition to the UN asserting that the US government was engaging in genocide against black people. The 1964 Malcolm X speech "The Ballot or the Bullet" also draws from "We Charge Genocide".

After World War II and following many years of mistreatment of African Americans by white Americans, the US government's official policies regarding this mistreatment shifted significantly. The American Civil Liberties Union (ACLU) said in 1946 that negative international opinion about US racial policies helped to pressure the US into alleviating the mistreatment of ethnic minorities. In 1948, President Harry S. Truman signed an order desegregating the military, and black citizens increasingly challenged other forms of racial discrimination. In 1948, even if African Americans worked side by side with their white counterparts, they were often segregated into separate neighborhoods due to redlining.

Lynching and other racial killings

Walter Johnson has written that the first lynching to occur in the United States was that of Francis McIntosh, a free man of black and white ancestry. He argued that this lynching ignited a series of them, all with the goal of "ethnic cleansing" and that Abraham Lincoln, who was not yet president, was more concerned by the vigilantism of the lynching than the murder itself. Lincoln referred to McIntosh as "obnoxious" in his 1838 speech later dubbed the Lyceum Address. According to the National Memorial for Peace and Justice 4,400 black people killed in lynchings and other racial killings between 1877 and 1950.

Brandy Marie Langley argued, "The physical killing of black people in America, at this time period, was consistent with Lemkin's original idea of genocide." Famous literary and social activist figures such as Mark Twain and Ida B. Wells were compelled to speak out about lynchings. Twain's essay about lynchings titled "The United States of Lyncherdom," a remark on widespread occurrence of lynchings in the US. According to Christopher Waldrep, the media and racist whites, both inadvertently and not, exaggerated the presence of black crime as a method of appeasing their own guilt surrounding the lynchings African Americans.

Sterilization

Further information: Eugenics in the United States

Beginning in 1907, some US state legislatures passed laws allowing for the compulsory sterilization of criminals, mentally retarded people, and institutionalized mentally ill patients. At first, African Americans and white Americans suffered sterilization in roughly equal ratio. By 1945, some 70,000 Americans had been sterilized in these programs. In the 1950s, the federal welfare program Aid to Families with Dependent Children (AFDC) was criticized by some whites who did not want to subsidize poor black families. States such as North and South Carolina performed sterilization procedures on low-income black mothers who were giving birth to their second child. The mothers were told that they would have to agree to have their tubes tied or their welfare benefits would be cancelled, along with the benefits of the families they were born into. Because of such policies, especially prevalent in Southern states, sterilization of African Americans in North Carolina increased from 23% of the total in the 1930s and 1940s to 59% at the end of the 1950s, and rose further to 64% in the mid-1960s.

In mid-1973 news stories revealed the forced sterilization of poor black women and children, paid for by federal funds. Two girls of the Relf family in Mississippi, deemed mentally incompetent at ages 12 and 14, and also 18-year-old welfare recipient Nial Ruth Cox of North Carolina, were prominent cases of involuntary sterilization. Jet magazine presented the story under the headline "Genocide". Critics said these stories were publicized by activists against legal abortion. According to Gregory Price, government policies led to higher rates of sterilization amongst black Americans than white on the basis of racist beliefs. He writes that in the early 1900s, the goal of eugenicists was to create a biologically fit population, but and that these standards of biological fitness deliberately excluded black people, who were claimed to not be capable of making legitimate contributions to the national economy.

Systemic racism as genocide

We Charge Genocide estimated 30,000 more black people died each year due to various racist policies and that black people had an 8-year shorter life span than white Americans. In this vein, Historian Matthew White estimates that 3.3 million more non-white people died from 1900 up to the 1960s than they would have if they had died at the same rate as white people.

Effects of wars on black communities

See also: Military history of African Americans and Racial discrimination against African Americans in the U.S. Military

African Americans pushed for equal participation in US military service in the first part of the 20th century and especially during World War II. Finally, President Harry S. Truman signed legislation to integrate the US military in 1948. However, Selective Service System deferments, military assignments, and especially the recruits accepted through Project 100,000 resulted in a greater representation of blacks in combat in the Vietnam War in the second half of the 1960s. African Americans represented 11% of the US population but 12.6% of troops sent to Vietnam. Cleveland Sellers said that the drafting of poor black men into war was "a plan to commit calculated genocide". Former SNCC chairman Stokely Carmichael, black congressman Adam Clayton Powell Jr. and SNCC member Rap Brown agreed. In October 1969, King's widow Coretta Scott King spoke at an anti-war protest held at the primarily black Morgan State College in Baltimore. Campus leaders published a statement against what they termed "black genocide" in Vietnam, blaming US President Richard Nixon as well as South Vietnamese leaders President Nguyễn Văn Thiệu and Vice President Nguyễn Cao Kỳ.

Author James Forman Jr. has called the War on Drugs "a misstep [that] is so damaging that future generations are left shaking their heads in disbelief." According to Forman, the war on drugs has had widespread effects, including an increased punitory criminal justice system that disproportionately affected Black Americans, especially those in low-income neighborhoods. Forman further writes that one consequence is that, even though black and white people have similar rates of drug use, black people are more likely to be punished for it by the judicial system.

Elizabeth Hinton writes that two other "wars" that have had detrimental effects on the black community – the War on Poverty and War on Crime. According to Hinton black men are imprisoned at a rate of 1 in 11. This topic is also explored in Michelle Alexander's The New Jim Crow. Alexander argues that, despite many Americans wanting to believe that the election of President Obama ushered in a new age where race no longer mattered, or at least not as much, America is still deeply affected by its racial history. Alexander writes that there has been a "systemic breakdown of black and poor communities devastated by mass unemployment, social neglect, economic abandonment, and intense police surveillance." President Lyndon B. Johnson, stated in a commencement speech delivered at Howard University that there is a stark contrast between black and white poverty. Keeanga-Yamahtta Taylor writes that the contrast is a result of systemic injustices carried out over the course of centuries against the black community.

Prison

Further information: Incarceration in the United States § Ethnicity, and Race and crime in the United States

In 1969, H. Rap Brown wrote in his autobiography, Die Nigger Die!, that American courts "conspire to commit genocide" against blacks by putting a disproportionate number of them in prison. Political scientist Joy A. James wrote that "antiblack genocide" is the motivating force which explains the way that US prisons are filled largely with black prisoners. Author and former prisoner Mansfield B. Frazier contends that the rumor in American ghettos "that whites are secretly engaged in a program of genocide against the black race" is given "a measure of validity" by the number of "black men of child-producing age who are imprisoned for crimes for which men of other races are not.

The book New Directions for Youth Development describes the school-to-prison pipeline along with ways to end it. It states that "The public school system in the United States, like the country as a whole, is plagued by vast inequalities—that all too frequently are defined along lines of race and class." Over time, as schools have become harsher in enforcing their policies and disciplining students, the criminal justice system has also become harsher in dealing with children. The book states that "Since 1992, fortyfive states have passed laws making it easier to try juveniles as adults, and thirty-one have stiffened sanctions against youths for a variety of offenses".

The way in which certain drugs are criminalized also factors into the large disparities in involvement in the prison system between black and white communities. For instance "conviction for crack selling (more heavily sold and used by people of color) [results] in a sentence 100 times more severe than for selling the same amount of powder cocaine (more heavily sold and used by whites)."

Reproductive rights

Birth control

Although black women had been practising forms of birth control since their arrival in America, certain African-American leaders also taught that political power came with greater population and so opposed contraception. In 1934, Marcus Garvey and his Universal Negro Improvement Association resolved that birth control would lead to the eradication of black people, terming it "race suicide" (Roosevelt had made the same comment about white people in 1905).

The combined oral contraceptive pill, popularly known as "the Pill", was approved for sale as a medicine in US markets in 1957, and in 1961, the use of it for birth control was also approved. In 1962, civil rights activist Whitney Young told the National Urban League not to support birth control for blacks. Marvin Davies, leader of the Florida chapter of the NAACP, said that black women should reject birth control and produce more babies so that black political influence would increase in the future.

Lyndon B. Johnson and Martin Luther King Jr., agreed that birth control was beneficial to poor black families.

Ideas of reproductive fitness were still at the center of American family planning in the 1960s. Physicians preferred to prescribe the Pill to white middle-class women and the IUD to poor women, especially poor women of color, because the IUD granted them greater control over "unfit" women's behavior. Guttmacher viewed the IUD as an effective method of contraception for individuals in "underdeveloped areas where two things are lacking: one, money and the other sustained motivation."

Once the method was approved for use in the United States, the majority of Pill users were white and middle-class women. In part, this trend reflects doctors' preference to prescribe the Pill to members of this population, and it also reflects the cost of the drug. Until the late 1960s, the Pill was prohibitively expensive for working-class and poor women.

After President Lyndon B. Johnson passed legislation for government funding of birth control as a part of his War on Poverty in 1964, Black activists such as Dr. Charles Greenlee and William "Bouie" Haden allied with social conservatives, such as Catholic priest Charles Owen Rice, to express concern about government-sponsored efforts to limit the Black population. Cecil B. Moore, head of the NAACP chapter in Philadelphia, spoke out against a Planned Parenthood effort to establish a stronger presence in northern Philadelphia; the population in the targeted neighborhoods was 70% black. Moore said that it would be "race suicide" if blacks embraced birth control.

H. Rap Brown said that black genocide was based on four factors, including birth control.

From 1965 to 1970, Black men aligned with conservative and religious groups—especially younger men from poverty-stricken areas—spoke out against birth control by denouncing it as part of a plot to commit a genocide against black people. The Black Panther Party and the Nation of Islam were the strongest critics of birth control. The Black Panther Party identified a number of injustices as factors which contributed to black genocide, including social ills that were more serious in black populations than they were in white populations, such as drug abuse, prostitution and sexually transmitted diseases. Other injustices included unsafe housing, malnutrition and the over-representation of young black men on the front lines of the Vietnam War. Influential black activists such as singer/author Julius Lester and comedian Dick Gregory said that blacks should increase the size of their population by avoiding genocidal family planning measures. H. Rap Brown of the Student Nonviolent Coordinating Committee (SNCC) held the view that black genocide consisted of four elements: more blacks executed than whites, malnutrition in impoverished areas affected blacks more than it affected whites, the Vietnam War killed more blacks than whites, and birth control programs in black neighborhoods were trying to end the black race. A birth control clinic in Cleveland, Ohio, was torched by black militants who stated that it contributed to black genocide.

Black Muslims said that birth control was against the teachings of the Koran, because in Muslim societies, the primary role of women is the production of children. In this context, the black Muslims believed that birth control was part of a genocidal attack which was being launched against them by whites. The Muslim weekly journal, Muhammad Speaks, contained many articles which demonized birth control.

In Newark, New Jersey, in July 1967, the Black power movement held its first convention: the National Conference on Black Power. The convention identified several means by which whites were attempting to annihilate blacks. Injustices in housing practices, reductions in welfare benefits, and government-subsidized family planning were all identified as elements of "black genocide". Ebony magazine printed a story in March 1968 in which it was revealed that poor blacks believed that a conspiracy to commit genocide against black people was the impetus behind government-funded birth control.

Reverend Martin Luther King Jr., was a strong proponent of birth control for blacks. In 1966, he won the Margaret Sanger Award in Human Rights, an award which honors the tireless birth control activism of Margaret Sanger, a co-founder of Planned Parenthood. King emphasized the fact that birth control gave the black man better command of his personal economic situation, keeping the number of his children within his monetary means. In April 1968, Martin Luther King Jr., was shot and killed. In 1971, Charles V. Willie wrote that among African Americans, this event marked the beginning of serious reflection "about the possibility of [black] genocide in America. There were lynchings, murders, and manslaughters in the past. But the assassination of Dr. King was too much. Many blacks believed that Dr. King had represented their best... If America could not accept Dr. King, then many felt that no black person in America was safe."

Angela Davis said that equating birth control with black genocide appeared to be "an exaggerated—even paranoiac—reaction."

Black women were generally critical of the Black Power Movement's rejection of birth control. In 1968, a group of black radical feminists in Mt. Vernon, New York issued "The Sisters Reply"; a rebuttal which said that birth control gave black women the "freedom to fight the genocide of black women and children," referring to the greater death rate among children and mothers in poor families. Frances M. Beal, co-founder of the Black Women's Liberation Committee of the SNCC, refused to believe that the black woman must be subservient to the black man's wishes. Angela Davis and Linda LaRue denounced the limitations which male Black Power activists imposed upon female Black Power activists, limitations which directed them to serve as mothers by producing "warriors for the revolution." Toni Cade said that indiscriminate births would not bring the liberation of blacks closer to realization; she advocated the use of the Pill as a tool to help black women space out the births of black children, to make it easier for families to raise them. The Black Women's Liberation Group accused "poor black men" of failing to support the babies which they helped produce, therefore supplying young black women with a reason to use contraceptives. Dara Abubakari, a black separatist, wrote that "women should be free to decide if and when they want children". A 1970 study found that 80% of black women in Chicago approved of birth control, and it also found that 75% of women were using it during their child-bearing years. A 1971 study found that a majority of black men and women were in favor of government-subsidized birth control.

In Pittsburgh, Pennsylvania, a community struggle both for and against the establishment of a birth control clinic in the Homewood area of east Pittsburgh made national news. Women in Pittsburgh had lobbied for the establishment of a birth control clinic in the 1920s and they were relieved when the American Birth Control League (ABCL) established one in 1931. The ABCL changed its name to Planned Parenthood in 1942. The Pittsburgh clinic initiated an educational outreach program to poor families in the Lower Hill District in 1956. This program was twinned into the poverty-stricken Homewood-Brushton area in 1958. Planned Parenthood considered opening another clinic there, and it conducted meetings with community leaders. In 1963 a mobile clinic was moved around the area. In December 1965, the Planned Parenthood Clinic of Pittsburgh (PPCP) applied for federal funding based on the War on Poverty legislation which Johnson had promoted. In May 1966, the application was approved, and the PPCP began to establish clinics throughout Pittsburgh, a total of 18 clinics were established throughout Pittsburgh by 1967, 11 of these clinics were placed in poor districts and they were also subsidized by the federal government. In mid-1966, the Pennsylvania state legislature held family planning funds up in committee. Catholic bishops gained media exposure for asserting that Pittsburgh's birth control efforts were a form of covert black genocide. In November 1966, the bishops said that the government was coercing poor people to have smaller families. Some black leaders such as local NAACP member Dr. Charles Greenlee supported the bishops' assertion that birth control was black genocide. Greenlee said that Planned Parenthood was "an honorable and good organization" but he also said that the federal Office of Economic Opportunity was sponsoring genocidal programs. Greenlee said that "the Negro's birth rate is the only weapon he has. When he reaches 21 he can vote." Greenlee targeted the Homewood clinic for closure; in doing so, he allied himself with black militant William "Bouie" Haden and Catholic prelate Charles Owen Rice in order to speak out against black genocide, and he also spoke out against the PPCP's educational outreach program. Planned Parenthood's Director of Community Relations Dr. Douglas Stewart said that the false charge of black genocide was harming the national advancement of blacks. In July 1968, Haden announced that he was willing to blow up the clinic in order to prevent it from operating. The Catholic church paid him a $10,000 salary, igniting an outcry in Pittsburgh's media. Bishop John Wright was called a "puppet of Bouie Haden". The PPCP closed the Homewood clinic in July 1968 and it also ended its educational program because it was concerned about violence. The black congregation of the Bethesda United Presbyterian Church issued a statement in which it said that accusations of black genocide were "patently false". A meeting to discuss the issue was scheduled for March 1969. About 200 women, mostly black, appeared in support of the clinic, and it was reopened. This event was seen as a major defeat for the black militant notion that government-funded birth control was black genocide.

Other prominent black advocates for birth control included Carl Rowan, James Farmer, Bayard Rustin, Jerome H. Holland, Ron Dellums and Barbara Jordan.

In the US in the 21st century, black women are most likely to be at risk for unintended pregnancies: 84% of black women of reproductive age use birth control, in contrast to 91% of Caucasian and Hispanic women, and 92% of Asian American women. This situation results in black women having the highest rate of unintended pregnancies—in 2001, almost 10% of black women who gave birth between the ages of 15 and 44 had unintended pregnancies, which was more than twice the rate of unintended pregnancies among white women. Poverty contributes to these statistics, because low-income women are more likely to experience disruptions in their lives; disruptions which affect the steady use of birth control. People who live in poor areas are more suspicious of the health care system, and as a result, they may reject medical treatment and advice, especially, they may reject less-critical wellness treatments such as birth control.

Abortion

Slave women brought with them from Africa the knowledge of traditional folk birth control practices, and of abortion obtained through the use of herbs, blunt trauma, and other methods of killing the fetus or producing strong uterine cramps. Slave women were often expected to breed more slave children to enrich their owners, but some quietly rebelled. In 1856 a white doctor reported that a number of slave owners were upset that their slaves appeared to hold a "secret by which they destroy the foetus at an early age of gestation". However, this folk knowledge was suppressed in the new American culture, especially by the nascent American Medical Association, and its practice fell away.

After slavery ended, black women formed social groups and clubs in the 1890s to "uplift their race." The revolutionary idea that a black woman might enjoy a full life without ever being a mother was presented in Josephine St. Pierre Ruffin's magazine The Woman's Era. Knowledge was secretly shared among clubwomen regarding how to find practitioners offering illegal medical or traditional abortion services. Working-class black women, who were more often forced into having sex with white men, continued to have a need for birth control and abortions. Black women who earned less than $10 per day paid $50 to $75 for an illegal and dangerous abortion. Throughout the 20th century, "backstreet" abortion providers in black neighborhoods were also sought out by poor white women who wanted to rid themselves of pregnancies. Abortion providers who were black were prosecuted much more often than white ones were.

During this time the Black Panthers printed pamphlets which described abortion as black genocide, expanding on their earlier stance with regard to family planning. However, most minority groups stood in favor of the decriminalization of abortion; The New York Times reported in 1970 that more non-white women than white women died as a result of "crude, illegal abortions". Legalized abortion was expected to produce fewer deaths of the mother. A poll in Buffalo, New York, conducted by the National Organization for Women (NOW), found that 75% of blacks supported the decriminalization of abortion.

In the 1970s, Jesse Jackson spoke out against abortion as a form of black genocide.

After the January 1973 Roe v. Wade Supreme Court decision made abortion legal in the US, Jet magazine publisher Robert E. Johnson authored an article titled "Legal Abortion: Is It Genocide Or Blessing In Disguise?" Johnson cast the issue as one which polarized the black community along gender lines: black women generally viewed abortion as a "blessing in disguise" but black men such as Reverend Jesse Jackson viewed it as black genocide. Jackson said he was in favor of birth control but not abortion. The next year, Senator Mark Hatfield, an opponent of legal abortion, emphasized to Congress that Jackson "regards abortion as a form of genocide practiced against blacks."

In Jet, Johnson quoted Lu Palmer, a radio journalist in Chicago, who said that there was inequity between the sexes: a young black man who helped create an unwanted pregnancy could go his "merry way" while the young woman who had been involved in it was stigmatized by society and saddled with a financial and emotional burden, often without a safety net of caregivers to sustain her. Civil rights lawyer Florynce Kennedy criticized the idea that black women were needed to populate the Black Power revolution. She said that black majorities in the Deep South were not known to be hotbeds of revolution, and that limiting black women to the role of mothers was "not too far removed from a cultural past where black women were encouraged to be breeding machines for their slave masters." In the Tennessee General Assembly in 1967, Dorothy Lavinia Brown, MD, the first African-American woman surgeon and a state assemblywoman, sponsored a proposed bill to fully legalize abortion. Later Brown, would say black women "should dispense quickly the notion that abortion is genocide." Rather, they should look to the earliest Atlantic slave traders as the root of genocide. Congresswoman Shirley Chisholm wrote in 1970 that the linking of abortion and genocide "is male rhetoric, for male ears."

However, a link between abortion and black genocide has been claimed by later observers. Mildred Fay Jefferson, a surgeon and an activist against legal abortion, wrote about black genocide in 1978, saying "abortionists have done more to get rid of generations and cripple others than all of the years of slavery and lynching." Jefferson's views were shared by Michigan state legislator and NAACP member Rosetta A. Ferguson, who led the effort to defeat a Michigan abortion liberalization bill in 1972. Ferguson described abortion as black genocide.

In 2009, American anti-abortion activists in Georgia revived the idea that a black genocide was in progress. A strong response from this strategy was observed among blacks, and in 2010 more focus was placed on describing abortion as black genocide. White anti-abortion activist Mark Crutcher produced a documentary called Maafa 21 which criticizes Planned Parenthood and its founder Margaret Sanger, and describes various historic aspects of eugenics, birth control and abortion with the aim of convincing the viewer that abortion is black genocide. Anti-abortion activists showed the documentary to black audiences across the US. The film was criticized as propaganda and a false representation of Sanger's work. In March 2011, a series of abortion-as-genocide billboard advertisements were shown in South Chicago, an area with a large population of African Americans. From May to November 2011, presidential candidate Herman Cain criticized Planned Parenthood, calling abortion "planned genocide" and "black genocide".

After Stacey Abrams lost the 2018 Georgia gubernatorial election, anti-abortion activist Arthur A. Goldberg wrote that she lost in part because of her stance in favor of abortion rights, which he said ignored "the staggering number of abortions in the black community" which amounted to black genocide. In 2019, The New York Times wrote that "the abortion debate is inextricably tied to race" in the view of black American communities that are challenged with many other racial disparities which together constitute black genocide.

A Pew Research Center survey found that black Americans favour legalized abortion for "most or all cases" at a rate of 68 percent, as opposed to 59 percent of white Americans.

Reception

The Civil Rights Congress (CRC)'s We Charge Genocide petition was popular almost everywhere in the world except in the United States. In 1952, one American writer visiting India found that many people had become familiar with the cases of the Martinsville Seven and Willie McGee through the document. The petition was particularly well received in Europe, where it received abundant press coverage.

The U.S. State Department requested that the NAACP draft a press release repudiating the petition, but the board decided against it. The NAACP felt the petition reflected many of the NAACP's own views, and even drew on NAACP data about lynchings other racist incidents. I. F. Stone was the only white American journalist to write favorably of the document. Raphael Lemkin, who invented the term "genocide", said the African-American population was increasing in size so could not be facing genocide. He also accused the CRC of working for foreign agents and of distracting from alleged genocides in the Soviet Union. The United Nations did not acknowledge receiving the petition, but the CRC had not expected it to, given the strength of U.S. influence.

In 1976, sociologist Irving Louis Horowitz published an analysis of black genocide in the United States. He says that genocide requires "conscious choice and policy" on behalf of the state, and that racist vigilantism and sporadic actions by individual whites were to blame for the various statistics which showed higher rates of death for black people than white people. Horowitz suggested that the U.S. government had not intentionally conspired to cause black genocide, and was only guilty of "benign neglect".

Critics of Horowitz, such as Seymour Drescher and Brandy Marie Langley, suggest there are contradictions in his analysis (e.g., he admits the KKK often had support from the police and state), and that his thesis fails because he uses only the Holocaust as a benchmark for genocide, which may be inappropriate or one-sided. Langley says that because state actors were "purposefully neglecting to recognize the dignity and [federal, constitutional] civil rights" of emancipated black people, such neglect was neither benign nor unintentional.

Historian Patrick Wolfe, a fellow of Harvard and Stanford, introduced the idea of "structural genocide", in which he suggests that non-physical forms of elimination can result in genocide – such as social, cultural and economic elimination – and that these can be ongoing processes as well as time-limited acts. He initially applied this model to explain Native American genocide, but extends it to cover other subjects of settler-colonial societies, including African Americans. Wolfe states that "elimination is an organizing principal of settler-colonial society rather than a one-off (and superseded) occurrence". He suggests that, because it is ongoing, the nature of this elimination can also change over time:

On emancipation, Blacks became surplus to some requirements and, to that extent, more like Indians. Thus it is highly significant that the barbarities of lynching and the Jim Crow reign of terror should be a post-emancipation phenomenon. As valuable commodities, slaves had only been destroyed in extremis. Even after slavery, Black people continued to have value as a source of super-cheap labour (providing an incitement to poor Whites), so their dispensability was tempered. Today in the US, the blatant racial zoning of large cities and the penal system suggests that, once colonized people outlive their utility, settler societies can fall back on the repertoire of strategies (in this case, spatial sequestration) whereby they have also dealt with the native surplus.

In 2013, political scientist Joy A. James wrote that the "logical conclusion" of racism in the United States is genocide, and that members of the black elite are complicit with white Americans in carrying out black genocide.

In 2021, Alex Hinton, director of the Center for the Study of Genocide and Human Rights at Rutgers University, says the original We Charge Genocide petition was "very compelling" but ahead of its time. He said, "While many may think that genocidal annihilation only looks like Nazi mass murder, the U.N. Genocide Convention clearly incorporates more nuanced forms of destruction than that." Like Wolfe, he suggests black genocide should be considered a form of structural genocide. He states that, despite Lemkin's objections, We Charge Genocide's claims were plausible according to Lemkin's own scholarship.