Genomics of domestication
Encyclopedia
Genomics is the study of the structure, content, and evolution
of genomes, or the entire genetic information of organisms. Domestication is the process by which humans alter the morphology and genes
of targeted organisms in order to select for desirable traits.
involves selection of traits over time, which leads to genetic changes, the science of genomics
can identify which genes across an entire genome are altered during this intense artificial selection
period. Understanding the genomics of domestication can also offer insight into the genetic effects of both the artificial
, human driven selection
of domestication, as well as natural selection
. This makes the genomics of domestication a unique tool for examining the genetics
of evolution in organisms that are relatively easy to study as their history may be more thoroughly preserved due to their usefulness to humans.
costs were prohibitive, this was limited to organisms with small genomes, such as viruses and bacteria, and then in eukaryotes, model organisms of importance to the scientific community for research. These included the Mus musculus (the house mouse), Drosophila melanogaster
(Fruit Fly) and Arabidopsis thaliana
(Arabidopsis) genomes. One of the most prominent publicly funded genome projects was the Human Genome Project
which helped to refine existing sequencing techniques as well as develop additional ones. Following these model organisms, agriculturally important species were next emphasized. As of 2009, there are more than 50 plant species whose genomes are being sequenced . However, the most important agricultural crops, including those in the grass and legume families such as rice
, wheat
and maize
, have received the most attention and funding. As of 2005, a full sequence of the rice genome has been published . These domesticated species and in some cases, their wild ancestors, have received focus due to their agricultural and economic importance and the benefits that having a sequenced genome for these species confers such as the ability to easily identify targets for selective breeding programs to increase yield, facilitate drought tolerance, or select a variety of desirable traits.
, reduced lateral branching, and an annual life cycle . The genes that code for these traits have been elucidated in some species, such as the maize tb1 gene, which controls for lateral branching, using classical genetic techniques as well as genomics. However, traditional Mendelian genetics which examines inheritance patters on an individual trait basis is limited to traits or phenotypes that cleanly segregate into distinct classes. Genomics is able to overcome this limitation through the comparison of the genomes
of individuals exhibiting a trait or phenotype of interest to a reference genome
which enables the identification differences between the two genomes such as Single Nucleotide Polymorphisms (SNPS), the movement of transposable elements (or retrotransposons) or deletions, among other genetic changes.
. By comparing the sequence of a previously isolated section of chromosome
8 in rice between fragrant and non-fragrant varietals researchers were able to determine their genetic difference. The aromatic and fragrant rice’s including Basmati
and Jasmine
are derived from an ancestral rice domesticate that suffered a deletion in exon
7 and as a result sequence coding for betaine aldehyde dehydrogenase (BADH2) was altered .
and mutations at these locations can prove fatal. Areas of the genome that are noncoding can be prone to much higher mutation rates. Because of this, these noncoding genes provide vital information when studying the divergence
of wild and domestic species. Since core genes are conserved between and among species, examining DNA sequences for these genes in multiple individuals of a species may be unable to provide much information on the diversity present in a population or species that is young. The estimated age of domesticated animal and plant species tends be less than 10,000 years, which on an evolutionary timescale, is relatively short . Because of this, highly variable noncoding DNA, such as Microsatellites, that mutate frequently, provide genetic markers with sufficient intraspecific variation to document domestication . Studying the noncoding DNA of domesticated species is made possible by genomics, which provides the genetic sequence of the entire genome, not simply coding DNA from genes of interest. In the case of coconuts
, recent genomic research using 10 microsatellite loci was able to determine that there have been 2 cases of coconut domestication based on sufficient variation between individuals found in the Indian Ocean
and those found in the Pacific Ocean
.
, allows researchers to compare DNA across multiple species and examine conserved sequences. In 2011, researchers at the Potato Genome Sequencing Consortium compared a de novo potato genome to 12 other species including, Arabidopsis, Grape
, Rice, Sorghum
, Maize, Popular
and others that allowed them to isolate potato specific genes, including those that confer resistance to potato blight caused by Phytophthora infestans
. The ability to predict genes of interest for crop breeding is a major advantage to the further domestication of crop species that is facilitated by genomics and the identification of genes and extragenic sequences that control for these desirable traits. Modern plant breeders can use this information to manipulate the genetics of crop species to develop new domesticated varieties with desired modern traits such as increased yield and the ability to respond better to nitrogen fertilizers
. Comparative genomics also allows researchers to make inferences about the evolution of life through comparing genomic sequences and examining patterns of divergence and conservation.
compared natural selection to domestication to help explain the former and he went on to write an entire book on the topic entitled The Variation of Animals and Plants under Domestication
. Domesticated species serve as ideal model systems for examining key concepts of evolution because their history is relatively short (on the evolutionary scale of billions of years) and well preserved. Additionally, by virtue of their usefulness to humans, many domesticated species are extant and available for study. The genomes of crop species have been sequenced in part to help with their improvement for agronomic
reasons, but because genome data are publicly available, in many cases for free, these organisms also serve as systems for examining the effects of evolution and artificial selection on genes. In particular, the genomics of domesticated species allow for the study of strong artificial selection
, founder events
and bottlenecks
, as well as wider evolutionary questions.
The process of domestication, by which only a choice few wild individuals are cultivated and selected against, often results in very strong selective pressures. This is evident in the genomes of these individuals as a lack of genetic diversity. In some cases this lack of diversity is seen as a selective sweep
, whereby the variation at a particular loci
of the genome is highly reduced while variation outside of this area is maintained or only partially reduced. In other cases, such as the coconut, genomic studies have reveled occurrences of a founder event, whereby the genetic diversity of an entire population is reduced due to a small number of individuals with low diversity being the isolated ancestors of a larger modern population . Bottlenecks, where variation is reduced throughout the entire genome, are also evident in crop species such as pearl millet
, cotton
, common bean
and lima bean
. With the identification of bottlenecks in these species, researchers are able to study the effects on an organisms’ ability to evolve past a bottleneck, and what effects this may have on the genomes of both individuals and populations as well as their fitness
.
and genetically, the Asian and African bottle gourds are sufficiently different to be designated as two separate subspecies
. Morphologically the American gourd resembles the African gourds more than the Asian gourds, which was previously used as support for the theory that the American variety is derived from a wild African gourd that floated across the ocean. However, in 2005 researchers with the Smithsonian Institution
were able to use a combination of archeological and genomic data to show that the bottle gourds in the Americas are actually more similar to Asian gourds, which suggests that the American gourds may be derived from Asian gourds that were carried across the Bering land bridge by Paleo-Indians .
(Coco nucifera L.) has shed light on the movements of Austronesian peoples. By examining 10 microsatelite loci, researchers found that there are 2 genetically distinct supopulations of coconut – one originating in the Indian Ocean, the Other in the Pacific Ocean. However, there is evidence of admixture
, the transfer of genetic material, between the two populations. Given that coconuts are ideally suited for ocean dispersal, it seems possible that individuals from one population could have floated to the other. However, the locations of the admixture events are limited to Madagascar
and coastal east Africa and exclude the Seychelles
. This pattern coincides with the known trade routes of Austronesian sailors. Additionally, there is a genetically distinct subpopulation of coconut on the eastern coast of South America which has undergone a genetic bottleneck resulting from a founder effect, however its ancestral population is the pacific coconut which suggests that Austronesian peoples may have sailed as far east as the Americas
Evolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
of genomes, or the entire genetic information of organisms. Domestication is the process by which humans alter the morphology and genes
Gênes
Gênes is the name of a département of the First French Empire in present Italy, named after the city of Genoa. It was formed in 1805, when Napoleon Bonaparte occupied the Republic of Genoa. Its capital was Genoa, and it was divided in the arrondissements of Genoa, Bobbio, Novi Ligure, Tortona and...
of targeted organisms in order to select for desirable traits.
Background
Since DomesticationDomestication
Domestication or taming is the process whereby a population of animals or plants, through a process of selection, becomes accustomed to human provision and control. In the Convention on Biological Diversity a domesticated species is defined as a 'species in which the evolutionary process has been...
involves selection of traits over time, which leads to genetic changes, the science of genomics
Genomics
Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...
can identify which genes across an entire genome are altered during this intense artificial selection
Artificial selection
Artificial selection describes intentional breeding for certain traits, or combination of traits. The term was utilized by Charles Darwin in contrast to natural selection, in which the differential reproduction of organisms with certain traits is attributed to improved survival or reproductive...
period. Understanding the genomics of domestication can also offer insight into the genetic effects of both the artificial
Artificial selection
Artificial selection describes intentional breeding for certain traits, or combination of traits. The term was utilized by Charles Darwin in contrast to natural selection, in which the differential reproduction of organisms with certain traits is attributed to improved survival or reproductive...
, human driven selection
Selection
In the context of evolution, certain traits or alleles of genes segregating within a population may be subject to selection. Under selection, individuals with advantageous or "adaptive" traits tend to be more successful than their peers reproductively—meaning they contribute more offspring to the...
of domestication, as well as natural selection
Natural selection
Natural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution....
. This makes the genomics of domestication a unique tool for examining the genetics
Genetics
Genetics , a discipline of biology, is the science of genes, heredity, and variation in living organisms....
of evolution in organisms that are relatively easy to study as their history may be more thoroughly preserved due to their usefulness to humans.
Genomics as a Tool
Historically genomic studies have been focused on select organisms for which there is funding to study. Initially, when sequencingDNA sequencing
DNA sequencing includes several methods and technologies that are used for determining the order of the nucleotide bases—adenine, guanine, cytosine, and thymine—in a molecule of DNA....
costs were prohibitive, this was limited to organisms with small genomes, such as viruses and bacteria, and then in eukaryotes, model organisms of importance to the scientific community for research. These included the Mus musculus (the house mouse), Drosophila melanogaster
Drosophila melanogaster
Drosophila melanogaster is a species of Diptera, or the order of flies, in the family Drosophilidae. The species is known generally as the common fruit fly or vinegar fly. Starting from Charles W...
(Fruit Fly) and Arabidopsis thaliana
Arabidopsis thaliana
Arabidopsis thaliana is a small flowering plant native to Europe, Asia, and northwestern Africa. A spring annual with a relatively short life cycle, arabidopsis is popular as a model organism in plant biology and genetics...
(Arabidopsis) genomes. One of the most prominent publicly funded genome projects was the Human Genome Project
Human Genome Project
The Human Genome Project is an international scientific research project with a primary goal of determining the sequence of chemical base pairs which make up DNA, and of identifying and mapping the approximately 20,000–25,000 genes of the human genome from both a physical and functional...
which helped to refine existing sequencing techniques as well as develop additional ones. Following these model organisms, agriculturally important species were next emphasized. As of 2009, there are more than 50 plant species whose genomes are being sequenced . However, the most important agricultural crops, including those in the grass and legume families such as rice
Rice
Rice is the seed of the monocot plants Oryza sativa or Oryza glaberrima . As a cereal grain, it is the most important staple food for a large part of the world's human population, especially in East Asia, Southeast Asia, South Asia, the Middle East, and the West Indies...
, wheat
Wheat
Wheat is a cereal grain, originally from the Levant region of the Near East, but now cultivated worldwide. In 2007 world production of wheat was 607 million tons, making it the third most-produced cereal after maize and rice...
and maize
Maize
Maize known in many English-speaking countries as corn or mielie/mealie, is a grain domesticated by indigenous peoples in Mesoamerica in prehistoric times. The leafy stalk produces ears which contain seeds called kernels. Though technically a grain, maize kernels are used in cooking as a vegetable...
, have received the most attention and funding. As of 2005, a full sequence of the rice genome has been published . These domesticated species and in some cases, their wild ancestors, have received focus due to their agricultural and economic importance and the benefits that having a sequenced genome for these species confers such as the ability to easily identify targets for selective breeding programs to increase yield, facilitate drought tolerance, or select a variety of desirable traits.
Genetics and Genomics of Domestication
During domestication, crop species undergo intense selective pressures that alter their genomes. The process of selection during domestication has largely focused on core traits that have come to define domesticated species. In seed or grain crops, these hallmark traits include increases in seed size, a reduction in natural seed dispersalSeed dispersal
Seed dispersal is the movement or transport of seeds away from the parent plant. Plants have limited mobility and consequently rely upon a variety of dispersal vectors to transport their propagules, including both abiotic and biotic vectors. Seeds can be dispersed away from the parent plant...
, reduced lateral branching, and an annual life cycle . The genes that code for these traits have been elucidated in some species, such as the maize tb1 gene, which controls for lateral branching, using classical genetic techniques as well as genomics. However, traditional Mendelian genetics which examines inheritance patters on an individual trait basis is limited to traits or phenotypes that cleanly segregate into distinct classes. Genomics is able to overcome this limitation through the comparison of the genomes
Comparative genomics
Comparative genomics is the study of the relationship of genome structure and function across different biological species or strains. Comparative genomics is an attempt to take advantage of the information provided by the signatures of selection to understand the function and evolutionary...
of individuals exhibiting a trait or phenotype of interest to a reference genome
Reference genome
A reference genome is a digital nucleic acid sequence database, assembled by scientists as a representative example of a species' genetic code. As they are often assembled from the sequencing of DNA from a number of donors, reference genomes do not accurately represent the genetic code of any...
which enables the identification differences between the two genomes such as Single Nucleotide Polymorphisms (SNPS), the movement of transposable elements (or retrotransposons) or deletions, among other genetic changes.
Coding DNA
Genomics offers insight into coding DNA as well as noncoding DNANoncoding DNA
In genetics, noncoding DNA describes components of an organism's DNA sequences that do not encode for protein sequences. In many eukaryotes, a large percentage of an organism's total genome size is noncoding DNA, although the amount of noncoding DNA, and the proportion of coding versus noncoding...
. By comparing the sequence of a previously isolated section of chromosome
Chromosome
A chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.Chromosomes...
8 in rice between fragrant and non-fragrant varietals researchers were able to determine their genetic difference. The aromatic and fragrant rice’s including Basmati
Basmati
Basmati is a variety of long grain rice grown in India, Bangladesh and Pakistan, notable for its fragrance and delicate, nuanced flavour. Its name means "the fragrant one" in Sanskrit, but it can also mean "the soft rice," and the word coincidentally means "my smile" in Arabic...
and Jasmine
Jasmine rice
Jasmine rice , sometimes known as Thai fragrant rice, is a long-grain variety of rice that has a nutty aroma and a subtle pandan-like flavor caused by 2-acetyl-1-pyrroline.Jasmine rice is originally from Thailand...
are derived from an ancestral rice domesticate that suffered a deletion in exon
Exon
An exon is a nucleic acid sequence that is represented in the mature form of an RNA molecule either after portions of a precursor RNA have been removed by cis-splicing or when two or more precursor RNA molecules have been ligated by trans-splicing. The mature RNA molecule can be a messenger RNA...
7 and as a result sequence coding for betaine aldehyde dehydrogenase (BADH2) was altered .
Noncoding DNA
However, looking solely at genes, or coding DNA, can be ineffective when examining certain traits or studying the evolution of a species during the domestication process. Genes that are vital for cellular process are often highly conservedConserved sequence
In biology, conserved sequences are similar or identical sequences that occur within nucleic acid sequences , protein sequences, protein structures or polymeric carbohydrates across species or within different molecules produced by the same organism...
and mutations at these locations can prove fatal. Areas of the genome that are noncoding can be prone to much higher mutation rates. Because of this, these noncoding genes provide vital information when studying the divergence
Genetic divergence
Genetic divergence is the process in which two or more populations of an ancestral species accumulate independent genetic changes through time, often after the populations have become reproductively isolated for some period of time...
of wild and domestic species. Since core genes are conserved between and among species, examining DNA sequences for these genes in multiple individuals of a species may be unable to provide much information on the diversity present in a population or species that is young. The estimated age of domesticated animal and plant species tends be less than 10,000 years, which on an evolutionary timescale, is relatively short . Because of this, highly variable noncoding DNA, such as Microsatellites, that mutate frequently, provide genetic markers with sufficient intraspecific variation to document domestication . Studying the noncoding DNA of domesticated species is made possible by genomics, which provides the genetic sequence of the entire genome, not simply coding DNA from genes of interest. In the case of coconuts
COcOnuts
COcOnuts is the second album released by Jane, comprising Animal Collective member Panda Bear, and Scott Mou. It was originally self-released on CD-R's, but later became the first album released by Psych-o-path Records in 2005. The Psych-o-path version was remastered by Rusty Santos and Edik Kleyner....
, recent genomic research using 10 microsatellite loci was able to determine that there have been 2 cases of coconut domestication based on sufficient variation between individuals found in the Indian Ocean
Indian Ocean
The Indian Ocean is the third largest of the world's oceanic divisions, covering approximately 20% of the water on the Earth's surface. It is bounded on the north by the Indian Subcontinent and Arabian Peninsula ; on the west by eastern Africa; on the east by Indochina, the Sunda Islands, and...
and those found in the Pacific Ocean
Pacific Ocean
The Pacific Ocean is the largest of the Earth's oceanic divisions. It extends from the Arctic in the north to the Southern Ocean in the south, bounded by Asia and Australia in the west, and the Americas in the east.At 165.2 million square kilometres in area, this largest division of the World...
.
Advantages of Genomics over Traditional Genetics
Genomics offers various benefits that the study of single genes, or genetics, does not. Having a fully sequenced genome for an organism, such as potatoPotato
The potato is a starchy, tuberous crop from the perennial Solanum tuberosum of the Solanaceae family . The word potato may refer to the plant itself as well as the edible tuber. In the region of the Andes, there are some other closely related cultivated potato species...
, allows researchers to compare DNA across multiple species and examine conserved sequences. In 2011, researchers at the Potato Genome Sequencing Consortium compared a de novo potato genome to 12 other species including, Arabidopsis, Grape
Grape
A grape is a non-climacteric fruit, specifically a berry, that grows on the perennial and deciduous woody vines of the genus Vitis. Grapes can be eaten raw or they can be used for making jam, juice, jelly, vinegar, wine, grape seed extracts, raisins, molasses and grape seed oil. Grapes are also...
, Rice, Sorghum
Sorghum
Sorghum is a genus of numerous species of grasses, one of which is raised for grain and many of which are used as fodder plants either cultivated or as part of pasture. The plants are cultivated in warmer climates worldwide. Species are native to tropical and subtropical regions of all continents...
, Maize, Popular
Popular
Popular may in various ways refer to:*an adjective referring to any people or population*Social status, the quality of being well-liked or well-known*Popularity, the quality of being well-liked...
and others that allowed them to isolate potato specific genes, including those that confer resistance to potato blight caused by Phytophthora infestans
Phytophthora infestans
Phytophthora infestans is an oomycete that causes the serious potato disease known as late blight or potato blight. . Late blight was a major culprit in the 1840s European, the 1845 Irish and 1846 Highland potato famines...
. The ability to predict genes of interest for crop breeding is a major advantage to the further domestication of crop species that is facilitated by genomics and the identification of genes and extragenic sequences that control for these desirable traits. Modern plant breeders can use this information to manipulate the genetics of crop species to develop new domesticated varieties with desired modern traits such as increased yield and the ability to respond better to nitrogen fertilizers
Fertilizer
Fertilizer is any organic or inorganic material of natural or synthetic origin that is added to a soil to supply one or more plant nutrients essential to the growth of plants. A recent assessment found that about 40 to 60% of crop yields are attributable to commercial fertilizer use...
. Comparative genomics also allows researchers to make inferences about the evolution of life through comparing genomic sequences and examining patterns of divergence and conservation.
Genomics of Domestication and Evolution
In his most famous work, Origin of Species, Charles DarwinCharles Darwin
Charles Robert Darwin FRS was an English naturalist. He established that all species of life have descended over time from common ancestry, and proposed the scientific theory that this branching pattern of evolution resulted from a process that he called natural selection.He published his theory...
compared natural selection to domestication to help explain the former and he went on to write an entire book on the topic entitled The Variation of Animals and Plants under Domestication
The Variation of Animals and Plants under Domestication
The Variation of Animals and Plants under Domestication is a book written by Charles Darwin that was first published in January 1868.A large proportion of the book contains detailed information on the domestication of animals and plants but it also contains in Chapter XXVII a description of...
. Domesticated species serve as ideal model systems for examining key concepts of evolution because their history is relatively short (on the evolutionary scale of billions of years) and well preserved. Additionally, by virtue of their usefulness to humans, many domesticated species are extant and available for study. The genomes of crop species have been sequenced in part to help with their improvement for agronomic
Agricultural economics
Agricultural economics originally applied the principles of economics to the production of crops and livestock — a discipline known as agronomics. Agronomics was a branch of economics that specifically dealt with land usage. It focused on maximizing the crop yield while maintaining a good soil...
reasons, but because genome data are publicly available, in many cases for free, these organisms also serve as systems for examining the effects of evolution and artificial selection on genes. In particular, the genomics of domesticated species allow for the study of strong artificial selection
Artificial selection
Artificial selection describes intentional breeding for certain traits, or combination of traits. The term was utilized by Charles Darwin in contrast to natural selection, in which the differential reproduction of organisms with certain traits is attributed to improved survival or reproductive...
, founder events
Founder effect
In population genetics, the founder effect is the loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population. It was first fully outlined by Ernst Mayr in 1942, using existing theoretical work by those such as Sewall...
and bottlenecks
Population bottleneck
A population bottleneck is an evolutionary event in which a significant percentage of a population or species is killed or otherwise prevented from reproducing....
, as well as wider evolutionary questions.
The process of domestication, by which only a choice few wild individuals are cultivated and selected against, often results in very strong selective pressures. This is evident in the genomes of these individuals as a lack of genetic diversity. In some cases this lack of diversity is seen as a selective sweep
Selective sweep
A selective sweep is the reduction or elimination of variation among the nucleotides in neighboring DNA of a mutation as the result of recent and strong positive natural selection....
, whereby the variation at a particular loci
Locus (genetics)
In the fields of genetics and genetic computation, a locus is the specific location of a gene or DNA sequence on a chromosome. A variant of the DNA sequence at a given locus is called an allele. The ordered list of loci known for a particular genome is called a genetic map...
of the genome is highly reduced while variation outside of this area is maintained or only partially reduced. In other cases, such as the coconut, genomic studies have reveled occurrences of a founder event, whereby the genetic diversity of an entire population is reduced due to a small number of individuals with low diversity being the isolated ancestors of a larger modern population . Bottlenecks, where variation is reduced throughout the entire genome, are also evident in crop species such as pearl millet
Pearl millet
Pearl millet is the most widely grown type of millet. Grown in Africa and the Indian subcontinent since prehistoric times, it is generally accepted that pearl millet originated in Africa and was subsequently introduced into India. The center of diversity, and suggested area of domestication, for...
, cotton
Cotton
Cotton is a soft, fluffy staple fiber that grows in a boll, or protective capsule, around the seeds of cotton plants of the genus Gossypium. The fiber is almost pure cellulose. The botanical purpose of cotton fiber is to aid in seed dispersal....
, common bean
Common bean
Phaseolus vulgaris, the common bean, is an herbaceous annual plant domesticated independently in ancient Mesoamerica and the Andes, and now grown worldwide for its edible bean, popular both dry and as a green bean. The leaf is occasionally used as a leaf vegetable, and the straw is used for fodder...
and lima bean
Lima bean
Phaseolus lunatus is a legume. It is grown for its seed, which is eaten as a vegetable. It is commonly known as the lima bean or butter bean.-Origin and uses:...
. With the identification of bottlenecks in these species, researchers are able to study the effects on an organisms’ ability to evolve past a bottleneck, and what effects this may have on the genomes of both individuals and populations as well as their fitness
Fitness (biology)
Fitness is a central idea in evolutionary theory. It can be defined either with respect to a genotype or to a phenotype in a given environment...
.
Domesticated Species and Human History
Domesticated species and the human populations that domesticate them are typified by a mutualistic relationship of interdependence . Domesticated crop species tend to become increasingly reliant on human populations for dispersal due to the selection against natural seed dispersal methods and humans have become increasingly dependent on domesticated crop species to sustain growing populations . Because many crop species rely on humans for dispersal, and it is possible to use genomics to track the dispersal of domesticated species, the genomics of domesticated species can be used as a tool to track human movements throughout history.Bottle gourd
The bottle gourd (lagenaria siceraria) is a domesticated species that originated in Africa and was dispersed throughout Asia by 9000 B.C.E. and reached the Americas by 8000 B.C.E. MorphologicallyMorphology (biology)
In biology, morphology is a branch of bioscience dealing with the study of the form and structure of organisms and their specific structural features....
and genetically, the Asian and African bottle gourds are sufficiently different to be designated as two separate subspecies
Subspecies
Subspecies in biological classification, is either a taxonomic rank subordinate to species, ora taxonomic unit in that rank . A subspecies cannot be recognized in isolation: a species will either be recognized as having no subspecies at all or two or more, never just one...
. Morphologically the American gourd resembles the African gourds more than the Asian gourds, which was previously used as support for the theory that the American variety is derived from a wild African gourd that floated across the ocean. However, in 2005 researchers with the Smithsonian Institution
Smithsonian Institution
The Smithsonian Institution is an educational and research institute and associated museum complex, administered and funded by the government of the United States and by funds from its endowment, contributions, and profits from its retail operations, concessions, licensing activities, and magazines...
were able to use a combination of archeological and genomic data to show that the bottle gourds in the Americas are actually more similar to Asian gourds, which suggests that the American gourds may be derived from Asian gourds that were carried across the Bering land bridge by Paleo-Indians .
Coconut
Genomic analysis of cultivated coconutCoconut
The coconut palm, Cocos nucifera, is a member of the family Arecaceae . It is the only accepted species in the genus Cocos. The term coconut can refer to the entire coconut palm, the seed, or the fruit, which is not a botanical nut. The spelling cocoanut is an old-fashioned form of the word...
(Coco nucifera L.) has shed light on the movements of Austronesian peoples. By examining 10 microsatelite loci, researchers found that there are 2 genetically distinct supopulations of coconut – one originating in the Indian Ocean, the Other in the Pacific Ocean. However, there is evidence of admixture
Genetic admixture
Genetic admixture occurs when individuals from two or more previously separated populations begin interbreeding. Admixture results in the introduction of new genetic lineages into a population. It has been known to slow local adaptation by introducing foreign, unadapted genotypes...
, the transfer of genetic material, between the two populations. Given that coconuts are ideally suited for ocean dispersal, it seems possible that individuals from one population could have floated to the other. However, the locations of the admixture events are limited to Madagascar
Madagascar
The Republic of Madagascar is an island country located in the Indian Ocean off the southeastern coast of Africa...
and coastal east Africa and exclude the Seychelles
Seychelles
Seychelles , officially the Republic of Seychelles , is an island country spanning an archipelago of 115 islands in the Indian Ocean, some east of mainland Africa, northeast of the island of Madagascar....
. This pattern coincides with the known trade routes of Austronesian sailors. Additionally, there is a genetically distinct subpopulation of coconut on the eastern coast of South America which has undergone a genetic bottleneck resulting from a founder effect, however its ancestral population is the pacific coconut which suggests that Austronesian peoples may have sailed as far east as the Americas