11 research outputs found
Diversity and Origins of Domestic Buffalo
River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil have been genotyped with the 90K Affymetrix Axiom® Buffalo Genotyping Array.
Geographic patterns of SNP diversity in pure river and pure swamp buffaloes confirm archeozoological data on the domestication of river buffalo in the Indian subcontinent and of swamp buffalo in Southeast Asia and provide hints on buffalo migrations and history.
In pure river buffalo three main gene pools are identified. One includes breeds from the Indian subcontinent (Pakistan) and those recently exported from there to Bulgaria, Brazil and Colombia; the second includes breeds that moved from the domestication center westwards (Iran, Egypt and Turkey); the third is formed by the Italian Mediterranea, recently exported to Mozambique. Mediterranea represents a highly differentiated gene pool due to bottlenecks, isolation, selection and possibly to genetic contributions from breeds not included in our sampling.
Four gene pools are identified in pure swamp buffalo. The first is in China; the second in Indonesian islands other than Sumatra; the third in the Philippines and the fourth in Thailand and Sumatra.
Some level of admixture between river and swamp is observed in the Philippines and in Brazil
Patterns of diversity in swamp and river buffalo as revealed by SNP molecular markers
After sequencing the Buffalo genome, the International Buffalo
Consortium has used the derived 90K Affymetrix Axiom® Buffalo
Genotyping Array to characterize a set of river buffaloes from
Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy,
Mozambique, Brazil and Colombia, and swamp buffaloes from
China, Thailand, Philippines, Indonesia and Brazil. SNP genotype
data have been analyzed with Bayesian clustering algorithms
(ADMIXTURE software), multivariate statistics (Multi-
Dimensional Scaling plots) and graph tools highlighting population
splits and migration events (TREEMIX software) to estimate
the levels of molecular diversity, population structure and the
historical relationships among populations. When placed in the
geographical context, the patterns of diversity confirmed archeozoological
evidence for the domestication of river and swamp
buffalo in the Indian subcontinent and in Southeast Asia, respectively,
and provided hints on buffalo migrations and history.
Admixture analysis revealed the presence of three main gene pools in pure river buffalo populations: one characterizes the
breeds from the Indian subcontinent (Pakistan) and those
recently exported from there to Bulgaria, Brazil and Colombia;
the second includes breeds that, from the domestication center,
spread westwards to Iran, Egypt and Turkey; the third includes
the Italian Mediterranean buffalo, sampled both in Italy and in
Mozambique where it has recently been exported. Among the
breeds analysed, Mediterranean buffalo represents the most differentiated
river buffalo gene pool, which is most likely due to
genetic bottlenecks, isolation, selection and possible genetic
contributions from breeds not included in our sampling. Four
gene pools have been identified in pure swamp buffalo populations:
the first from China; the second in Indonesian islands,
other than Sumatra; the third in the Philippines and the fourth
in Thailand and Sumatra. Some level of admixture is seen
between river and swamp buffalo in the Philippines and in
Brazil. TREEMIX software analyses confirmed the gene flows
identified by Bayesian population structure analysis including
those from the river buffalo gene pool to the admixed swamp
populations and, within river buffaloes, from the Mediterranean
to the breeds from Colombia and Brazil. Furthermore, these
analyses revealed some unexpected migration patterns, which
suggest that the westward spread of domestic buffaloes may have
followed alternative migration routes
Water buffalo genomic diversity and post-domestication migration routes.
The 90K Affymetrix Axiom® Buffalo Genotyping Array has been used to genotype river buffalo samples from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil. Model-based clustering algorithms (Admixture and FastStructure software) and graph tools (Treemix and network analysis) have been applied to SNP data to evaluate the levels of molecular diversity and to highlight population structure and migration events. The best-fitting resolution devised by Bayesian clustering highlighted three distinct gene pools in pure river as well as in pure swamp buffalo populations, together with some genomic admixture occurring in the Philippines and in Brazil, in agreement with documented importations of animals for breed improvement purposes. The Mediterranean buffalo and the Carabao breed from Brazil represent the most differentiated gene pools within the river and swamp group, respectively, which is most likely due to genetic bottlenecks, isolation and selection. Gene flow events, evidenced by Treemix and Network analyses, highlighted a likely contribution from the river buffalo gene pool to the admixed swamp populations and, within river buffaloes, from the Mediterranean to the breeds from Colombia and Brazil. When evaluated in a geographical framework, the results of our analyses support archeozoological evidence for the domestication of river and swamp buffalo in the Indian subcontinent and in Southeast Asia, respectively, and furthermore revealed some unexpected patterns of migration, which suggest that the spread of domestic buffaloes out of the domestication center may have followed alternative migration routes
New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data
The domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. The two types of water buffalo, i.e. river and swamp, display distinct morphological and behavioural traits, different karyotypes and also have different purposes and geographical distributions. River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil were genotyped with a species-specific medium-density 90K SNP panel. We estimated the levels of molecular diversity and described population structure, which revealed historical relationships between populations and migration events. Three distinct gene pools were identified in pure river as well as in pure swamp buffalo populations. Genomic admixture was seen in the Philippines and in Brazil, resulting from importations of animals for breed improvement. Our results were largely consistent with previous archaeological, historical and molecular-based evidence for two independent domestication events for river- and swamp-type buffaloes, which occurred in the Indo-Pakistani region and close to the China/Indochina border, respectively. Based on a geographical analysis of the distribution of diversity, our evidence also indicated that the water buffalo spread out of the domestication centres followed two major divergent migration directions: river buffaloes migrated west from the Indian sub-continent while swamp buffaloes migrated from northern Indochina via an east-south-eastern route. These data suggest that the current distribution of water buffalo diversity has been shaped by the combined effects of multiple migration events occurred at different stages of the post-domestication history of the species
Table1.XLSX
<p>The domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. The two types of water buffalo, i.e., river and swamp, display distinct morphological and behavioral traits, different karyotypes and also have different purposes and geographical distributions. River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil were genotyped with a species-specific medium-density 90K SNP panel. We estimated the levels of molecular diversity and described population structure, which revealed historical relationships between populations and migration events. Three distinct gene pools were identified in pure river as well as in pure swamp buffalo populations. Genomic admixture was seen in the Philippines and in Brazil, resulting from importations of animals for breed improvement. Our results were largely consistent with previous archeological, historical and molecular-based evidence for two independent domestication events for river- and swamp-type buffaloes, which occurred in the Indo-Pakistani region and close to the China/Indochina border, respectively. Based on a geographical analysis of the distribution of diversity, our evidence also indicated that the water buffalo spread out of the domestication centers followed two major divergent migration directions: river buffaloes migrated west from the Indian sub-continent while swamp buffaloes migrated from northern Indochina via an east-south-eastern route. These data suggest that the current distribution of water buffalo diversity has been shaped by the combined effects of multiple migration events occurred at different stages of the post-domestication history of the species.</p
DataSheet1.docx
<p>The domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. The two types of water buffalo, i.e., river and swamp, display distinct morphological and behavioral traits, different karyotypes and also have different purposes and geographical distributions. River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil were genotyped with a species-specific medium-density 90K SNP panel. We estimated the levels of molecular diversity and described population structure, which revealed historical relationships between populations and migration events. Three distinct gene pools were identified in pure river as well as in pure swamp buffalo populations. Genomic admixture was seen in the Philippines and in Brazil, resulting from importations of animals for breed improvement. Our results were largely consistent with previous archeological, historical and molecular-based evidence for two independent domestication events for river- and swamp-type buffaloes, which occurred in the Indo-Pakistani region and close to the China/Indochina border, respectively. Based on a geographical analysis of the distribution of diversity, our evidence also indicated that the water buffalo spread out of the domestication centers followed two major divergent migration directions: river buffaloes migrated west from the Indian sub-continent while swamp buffaloes migrated from northern Indochina via an east-south-eastern route. These data suggest that the current distribution of water buffalo diversity has been shaped by the combined effects of multiple migration events occurred at different stages of the post-domestication history of the species.</p
Table2.xlsx
<p>The domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. The two types of water buffalo, i.e., river and swamp, display distinct morphological and behavioral traits, different karyotypes and also have different purposes and geographical distributions. River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil were genotyped with a species-specific medium-density 90K SNP panel. We estimated the levels of molecular diversity and described population structure, which revealed historical relationships between populations and migration events. Three distinct gene pools were identified in pure river as well as in pure swamp buffalo populations. Genomic admixture was seen in the Philippines and in Brazil, resulting from importations of animals for breed improvement. Our results were largely consistent with previous archeological, historical and molecular-based evidence for two independent domestication events for river- and swamp-type buffaloes, which occurred in the Indo-Pakistani region and close to the China/Indochina border, respectively. Based on a geographical analysis of the distribution of diversity, our evidence also indicated that the water buffalo spread out of the domestication centers followed two major divergent migration directions: river buffaloes migrated west from the Indian sub-continent while swamp buffaloes migrated from northern Indochina via an east-south-eastern route. These data suggest that the current distribution of water buffalo diversity has been shaped by the combined effects of multiple migration events occurred at different stages of the post-domestication history of the species.</p