African and European mitochondrial haplotypes in South American Creole cattle

Ancient DNA confirms diverse origins of early post-Columbian cattle in the Americas

Before the arrival of Europeans, domestic cattle (Bos taurus) did not exist in the Americas, and most of our knowledge about how domestic bovines first arrived in the Western Hemisphere is based on historical documents. Sixteenth-century colonial accounts suggest that the first cattle were brought in small numbers from the southern Iberian Peninsula via the Canary archipelago to the Caribbean islands where they were bred locally and imported to other circum-Caribbean regions. Modern American heritage cattle genetics and limited ancient mtDNA data from archaeological colonial cattle suggest a more complex story of mixed ancestries from Europe and Africa. So far little information exists to understand the nature and timing of the arrival of these mixed-ancestry populations. In this study we combine ancient mitochondrial and nuclear DNA from a robust sample of some of the earliest archaeological specimens from Caribbean and Mesoamerican sites to clarify the origins and the dynamics of bovine introduction into the Americas. Our analyses support first arrival of cattle from diverse locales and potentially confirm the early arrival of African-sourced cattle in the Americas, followed by waves of later introductions from various sources over several centuries.

DNA Multi-Marker Genotyping and CIAS Morphometric Phenotyping of Fasciola gigantica-Sized Flukes from Ecuador, with an Analysis of the Radix Absence in the New World and the Evolutionary Lymnaeid Snail Vector Filter

Simple Summary

Fasciolid flukes collected from sheep and cattle in Ecuador showed a high diversity in DNA sequences whose analyses indicated introductions from South America, European and North American countries. These results agree with the numerous livestock importations performed by Ecuador. Abnormally big-sized liver flukes were found in Ecuadorian sheep. The morphometric phenotypic CIAS study showed that its size maximum and mean very pronouncedly and significantly surpassed those of the Fasciola hepatica populations from South America and Spain and proved to be intermediate between standard F. hepatica and F. gigantica populations. Such a feature is only known in intermediate fasciolid forms in Old World areas where the two species and their specific lymnaeid snail vectors overlap. This argues about a past hybridization after F. gigantica importation from Pakistan and/or introduction of intermediate hybrids previously generated in USA. The lack of heterozygotic rDNA ITS positions differentiating the two species, and of introgressed fragments and heteroplasmic positions in mtDNA genes, indicate a post-hybridization period sufficiently long as for rDNA concerted evolution to complete homogenization and mtDNA to return to homoplasmy. The vector specificity filter due to Radix absence should act as a driving force in accelerating such lineage evolution. Public health implications are finally emphasized.

Abstract

Fascioliasis is a disease caused by Fasciola hepatica worldwide transmitted by lymnaeid snails mainly of the Galba/Fossaria group and F. gigantica restricted to parts of Africa and Asia and transmitted by Radix lymnaeids. Concern has recently risen regarding the high pathogenicity and human infection capacity of F. gigantica. Abnormally big-sized fasciolids were found infecting sheep in Ecuador, the only South American country where F. gigantica has been reported. Their phenotypic comparison with F. hepatica infecting sheep from Peru, Bolivia and Spain, and F. gigantica from Egypt and Vietnam demonstrated the Ecuadorian fasciolids to have size-linked parameters of F. gigantica. Genotyping of these big-sized fasciolids by rDNA ITS-2 and ITS-1 and mtDNA cox1 and nad1 and their comparison with other countries proved the big-sized fasciolids to belong to F. hepatica. Neither heterozygotic ITS position differentiated the two species, and no introgressed fragments and heteroplasmic positions in mtDNA were found. The haplotype diversity indicates introductions mainly from other South American countries, Europe and North America. Big-sized fasciolids from Ecuador and USA are considered to be consequences of F.gigantica introductions by past livestock importations. The vector specificity filter due to Radix absence should act as driving force in the evolution in such lineages.

The genetic ancestry of American Creole cattle inferred from uniparental and autosomal genetic markers

Cattle imported from the Iberian Peninsula spread throughout America in the early years of discovery and colonization to originate Creole breeds, which adapted to a wide diversity of environments and later received influences from other origins, including zebu cattle in more recent years. We analyzed uniparental genetic markers and autosomal microsatellites in DNA samples from 114 cattle breeds distributed worldwide, including 40 Creole breeds representing the whole American continent, and samples from the Iberian Peninsula, British islands, Continental Europe, Africa and American zebu. We show that Creole breeds differ considerably from each other, and most have their own identity or group with others from neighboring regions. Results with mtDNA indicate that T1c-lineages are rare in Iberia but common in Africa and are well represented in Creoles from Brazil and Colombia, lending support to a direct African influence on Creoles. This is reinforced by the sharing of a unique Y-haplotype between cattle from Mozambique and Creoles from Argentina. Autosomal microsatellites indicate that Creoles occupy an intermediate position between African and European breeds, and some Creoles show a clear Iberian signature. Our results confirm the mixed ancestry of American Creole cattle and the role that African cattle have played in their development.

Resurrecting Darwin's Niata - anatomical, biomechanical, genetic, and morphometric studies of morphological novelty in cattle

The Niata was a cattle variety from South America that figured prominently in writings on evolution by Charles Darwin. Its shortened head and other aspects of its unusual morphology have been subject of unsettled discussions since Darwin’s time. Here, we examine the anatomy, cranial shape, skull biomechanics, and population genetics of the Niata. Our results show that the Niata was a viable variety of cattle and exhibited anatomical differences to known chondrodysplastic forms. In cranial shape and genetic analysis, the Niata occupies an isolated position clearly separated from other cattle. Computational biomechanical model comparison reveals that the shorter face of the Niata resulted in a restricted distribution and lower magnitude of stress during biting. Morphological and genetic data illustrate the acquisition of novelty in the domestication process and confirm the distinct nature of the Niata cattle, validating Darwin’s view that it was a true breed.

Dairy cattle serum and milk factors contributing to the risk of colon and breast cancers

The analysis of published epidemiological data on colon and breast cancer reveals a remarkable concordance for most regions of the world. A low incidence for both cancers has been recorded in Mongolia and Bolivia. Discrepant data, however, have been reported for India, Japan and Korea. In India, the incidence of breast cancer is significantly higher than for colon cancer, in Japan and Korea colon cancer exceeds by far the rate of breast cancer. Here, studies are summarized pointing to a species-specific risk for colon cancer after consumption of beef originating from dairy cattle. Uptake of dairy products of Bos taurus-derived milk cattle, particularly consumed at early age, is suggested to represent one of the main risk factors for the development of breast cancer. A recent demonstration of reduced breast cancer rates in individuals with lactose intolerance (Ji et al., Br J Cancer 2014; 112:149-52) seems to be in line with this interpretation. Species-specific risk factors for these cancers are compatible with the transmission of different infectious factors transferred via meat or dairy products. Countries with discordant rates of colon and breast cancer reveal a similar discordance between meat and milk product consumption of dairy cattle. The recent isolation of a larger number of novel presumably viral DNAs from serum, meat and dairy products of healthy dairy cows, at least part of them infectious for human cells, deserves further investigation. Systemic infections early in life, resulting in latency and prevention of subsequent infections with the same agent by neutralizing antibodies, would require reconsideration of ongoing prospective studies conducted in the adult population.

Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle

The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds and populations have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns of geographic dispersal resulting from co-migration with humans and exportation are recognizable in phylogenetic networks. All analytical methods reveal patterns of hybridization which occurred after divergence. Using 19 breeds, we map the cline of indicine introgression into Africa. We infer that African taurine possess a large portion of wild African auroch ancestry, causing their divergence from Eurasian taurine. We detect exportation patterns in Asia and identify a cline of Eurasian taurine/indicine hybridization in Asia. We also identify the influence of species other than Bos taurus taurus and B. t. indicus in the formation of Asian breeds. We detect the pronounced influence of Shorthorn cattle in the formation of European breeds. Iberian and Italian cattle possess introgression from African taurine. American Criollo cattle originate from Iberia, and not directly from Africa with African ancestry inherited via Iberian ancestors. Indicine introgression into American cattle occurred in the Americas, and not Europe. We argue that cattle migration, movement and trading followed by admixture have been important forces in shaping modern bovine genomic variation.

The DNA of domesticated plants and animals contains information about how species were domesticated, exported, and bred by early farmers. Modern breeds were developed by lengthy and complex processes; however, our use of 134 breeds and new analytical models enabled us to reveal some of the processes that created modern cattle diversity. In Asia, Africa, North and South America, humpless (Bos t. taurus or taurine) and humped (Bos t. indicus or indicine) cattle were crossbred to produce hybrids adapted to the environment and local production systems. The history of Asian cattle involves the domestication and admixture of several species whereas African taurines arose through the introduction of domesticated Fertile Crescent taurines and their hybridization with wild African aurochs. African taurine genetic background is commonly observed among European Mediterranean breeds. The absence of indicine introgression within most European taurine breeds, but presence within three Italian breeds is consistent with at least two separate migration waves of cattle to Europe, one from the Middle East which captured taurines in which indicine introgression had already occurred and the second from western Africa into Spain with no indicine introgression. This second group seems to have radiated from Spain into the Mediterranean resulting in a cline of African taurine introgression into European taurines.

Ancient mtDNA analysis of early 16(th) century Caribbean cattle provides insight into founding populations of New World creole cattle breeds

The Columbian Exchange resulted in a widespread movement of humans, plants and animals between the Old and New Worlds. The late 15^th to early 16^th century transfer of cattle from the Iberian Peninsula and Canary Islands to the Caribbean laid the foundation for the development of American creole cattle (Bos taurus) breeds. Genetic analyses of modern cattle from the Americas reveal a mixed ancestry of European, African and Indian origins. Recent debate in the genetic literature centers on the ‘African’ haplogroup T1 and its subhaplogroups, alternatively tying their origins to the initial Spanish herds, and/or from subsequent movements of taurine cattle through the African slave trade. We examine this problem through ancient DNA analysis of early 16^th century cattle bone from Sevilla la Nueva, the first Spanish colony in Jamaica. In spite of poor DNA preservation, both T3 and T1 haplogroups were identified in the cattle remains, confirming the presence of T1 in the earliest Spanish herds. The absence, however, of “African-derived American” haplotypes (AA/T1c1a1) in the Sevilla la Nueva sample, leaves open the origins of this sub-haplogroup in contemporary Caribbean cattle.

New World cattle show ancestry from multiple independent domestication events

Previous archeological and genetic research has shown that modern cattle breeds are descended from multiple independent domestication events of the wild aurochs (Bos primigenius) ∼10,000 y ago. Two primary areas of domestication in the Middle East/Europe and the Indian subcontinent resulted in taurine and indicine lines of cattle, respectively. American descendants of cattle brought by European explorers to the New World beginning in 1493 generally have been considered to belong to the taurine lineage. Our analyses of 47,506 single nucleotide polymorphisms show that these New World cattle breeds, as well as many related breeds of cattle in southern Europe, actually exhibit ancestry from both the taurine and indicine lineages. In this study, we show that, although European cattle are largely descended from the taurine lineage, gene flow from African cattle (partially of indicine origin) contributed substantial genomic components to both southern European cattle breeds and their New World descendants. New World cattle breeds, such as Texas Longhorns, provide an opportunity to study global population structure and domestication in cattle. Following their introduction into the Americas in the late 1400s, semiferal herds of cattle underwent between 80 and 200 generations of predominantly natural selection, as opposed to the human-mediated artificial selection of Old World breeding programs. Our analyses of global cattle breed population history show that the hybrid ancestry of New World breeds contributed genetic variation that likely facilitated the adaptation of these breeds to a novel environment.

Genetic footprints of Iberian cattle in America 500 years after the arrival of Columbus

Background

American Creole cattle presumably descend from animals imported from the Iberian Peninsula during the period of colonization and settlement, through different migration routes, and may have also suffered the influence of cattle directly imported from Africa. The introduction of European cattle, which began in the 18th century, and later of Zebu from India, has threatened the survival of Creole populations, some of which have nearly disappeared or were admixed with exotic breeds. Assessment of the genetic status of Creole cattle is essential for the establishment of conservation programs of these historical resources.

Methodology/Principal Findings

We sampled 27 Creole populations, 39 Iberian, 9 European and 6 Zebu breeds. We used microsatellite markers to assess the origins of Creole cattle, and to investigate the influence of different breeds on their genetic make-up. The major ancestral contributions are from breeds of southern Spain and Portugal, in agreement with the historical ports of departure of ships sailing towards the Western Hemisphere. This Iberian contribution to Creoles may also include some African influence, given the influential role that African cattle have had in the development of Iberian breeds, but the possibility of a direct influence on Creoles of African cattle imported to America can not be discarded. In addition to the Iberian influence, the admixture with other European breeds was minor. The Creoles from tropical areas, especially those from the Caribbean, show clear signs of admixture with Zebu.

Conclusions/Significance

Nearly five centuries since cattle were first brought to the Americas, Creoles still show a strong and predominant signature of their Iberian ancestors. Creole breeds differ widely from each other, both in genetic structure and influences from other breeds. Efforts are needed to avoid their extinction or further genetic erosion, which would compromise centuries of selective adaptation to a wide range of environmental conditions.

Origin and spread of Bos taurus: new clues from mitochondrial genomes belonging to haplogroup T1

Background

Most genetic studies on modern cattle have established a common origin for all taurine breeds in the Near East, during the Neolithic transition about 10 thousand years (ka) ago. Yet, the possibility of independent and/or secondary domestication events is still debated and is fostered by the finding of rare mitochondrial DNA (mtDNA) haplogroups like P, Q and R. Haplogroup T1, because of its geographic distribution, has been the subject of several investigations pointing to a possible independent domestication event in Africa and suggesting a genetic contribution of African cattle to the formation of Iberian and Creole cattle. Whole mitochondrial genome sequence analysis, with its proven effectiveness in improving the resolution of phylogeographic studies, is the most appropriate tool to investigate the origin and structure of haplogroup T1.

Methodology

A survey of >2200 bovine mtDNA control regions representing 28 breeds (15 European, 10 African, 3 American) identified 281 subjects belonging to haplogroup T1. Fifty-four were selected for whole mtDNA genome sequencing, and combined with ten T1 complete sequences from previous studies into the most detailed T1 phylogenetic tree available to date.

Conclusions

Phylogenetic analysis of the 64 T1 mitochondrial complete genomes revealed six distinct sub-haplogroups (T1a–T1f). Our data support the overall scenario of a Near Eastern origin of the T1 sub-haplogroups from as much as eight founding T1 haplotypes. However, the possibility that one sub-haplogroup (T1d) arose in North Africa, in domesticated stocks, shortly after their arrival from the Near East, can not be ruled out. Finally, the previously identified “African-derived American" (AA) haplotype turned out to be a sub-clade of T1c (T1c1a1). This haplotype was found here for the first time in Africa (Egypt), indicating that it probably originated in North Africa, reached the Iberian Peninsula and sailed to America, with the first European settlers.

Lymnaea schirazensis, an overlooked snail distorting fascioliasis data: genotype, phenotype, ecology, worldwide spread, susceptibility, applicability

BACKGROUND

Lymnaeid snails transmit medical and veterinary important trematodiases, mainly fascioliasis. Vector specificity of fasciolid parasites defines disease distribution and characteristics. Different lymnaeid species appear linked to different transmission and epidemiological patterns. Pronounced susceptibility differences to absolute resistance have been described among lymnaeid populations. When assessing disease characteristics in different endemic areas, unexpected results were obtained in studies on lymnaeid susceptibility to Fasciola. We undertook studies to understand this disease transmission heterogeneity.

METHODOLOGY/PRINCIPAL FINDINGS

A ten-year study in Iran, Egypt, Spain, the Dominican Republic, Mexico, Venezuela, Ecuador and Peru, demonstrated that such heterogeneity is not due to susceptibility differences, but to a hitherto overlooked cryptic species, Lymnaea schirazensis, confused with the main vector Galba truncatula and/or other Galba/Fossaria vectors. Nuclear rDNA and mtDNA sequences and phylogenetic reconstruction highlighted an old evolutionary divergence from other Galba/Fossaria species, and a low intraspecific variability suggesting a recent spread from one geographical source. Morphometry, anatomy and egg cluster analyses allowed for phenotypic differentiation. Selfing, egg laying, and habitat characteristics indicated a migration capacity by passive transport. Studies showed that it is not a vector species (n = 8572 field collected, 20 populations): snail finding and penetration by F. hepatica miracidium occur but never lead to cercarial production (n = 338 experimentally infected).

CONCLUSIONS/SIGNIFICANCE

This species has been distorting fasciolid specificity/susceptibility and fascioliasis geographical distribution data. Hence, a large body of literature on G. truncatula should be revised. Its existence has henceforth to be considered in research. Genetic data on livestock, archeology and history along the 10,000-year post-domestication period explain its wide spread from the Neolithic Fertile Crescent. It is an efficient biomarker for the follow-up of livestock movements, a crucial aspect in fascioliasis emergence. It offers an outstanding laboratory model for genetic studies on susceptibility/resistance in F. hepatica/lymnaeid interaction, a field of applied research with disease control perspectives.

Genetic diversity in farm animals--a review

Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected to benefit from advances in molecular technology.

Origins and genetic diversity of New World Creole cattle: inferences from mitochondrial and Y chromosome polymorphisms

The ancestry of New World cattle was investigated through the analysis of mitochondrial and Y chromosome variation in Creoles from Argentina, Brazil, Mexico, Paraguay and the United States of America. Breeds that influenced the Creoles, such as Iberian native, British and Zebu, were also studied. Creoles showed high mtDNA diversity (H = 0.984 +/- 0.003) with a total of 78 haplotypes, and the European T3 matriline was the most common (72.1%). The African T1a haplogroup was detected (14.6%), as well as the ancestral African-derived AA matriline (11.9%), which was absent in the Iberian breeds. Genetic proximity among Creoles, Iberian and Atlantic Islands breeds was inferred through their sharing of mtDNA haplotypes. Y-haplotype diversity in Creoles was high (H = 0.779 +/- 0.019), with several Y1, Y2 and Y3 haplotypes represented. Iberian patrilines in Creoles were more difficult to infer and were reflected by the presence of H3Y1 and H6Y2. Y-haplotypes confirmed crossbreeding with British cattle, mainly of Hereford with Pampa Chaqueño and Texas Longhorn. Male-mediated Bos indicus introgression into Creoles was found in all populations, except Argentino1 (herd book registered) and Pampa Chaqueño. The detection of the distinct H22Y3 patriline with the INRA189-90 allele in Caracú suggests introduction of bulls directly from West Africa. Further studies of Spanish and African breeds are necessary to elucidate the origins of Creole cattle, and determine the exact source of their African lineages.

[Genetic diversity and origin of mitochondria DNA D-loop region of some Chinese indigenous cattle breeds]

The complete D-loop region of mitochondrial DNA from 206 individuals in 16 Chinese indigenous cattle breeds was sequenced and analyzed to detect variability of D-loop region of mitochondria DNA for those breeds. The results showed as follows: 101 variations and 99 haplotypes were found, in which 73 haplotypes were of Bos taurus and the other 26 haplotypes were of Bos indicus, and the average number of nucleotide differences was 22.6920, haplotype diversity was 0.9320, and nucleotide diversity was 0.0227, indicating high genetic diversity in Chinese indigenous cattle breeds. According to the NJ phylogenetic tree, 16 cattle breeds were divided into two clades, Bos taurus and Bos indicus. Based on the Network graphics, the 73 haplotypes of Bos taurus were classified into 3 groups and the 26 haplotypes of Bos indicus were classified into 5 groups. It was inferred that cattle breeds of Bos indicus in China had experienced at least 4 population expansions during their movement. There was only 16% of H3 haplotype sequences similar to the sequence of Nellore, and 84% of those sequences had purine C variation in Chinese indigenous cattle breeds through the analysis on their common H3 haplotypes. It was concluded that those purine C decrease was possibly originated in Chinese Bos indicus.

African matrilineages in American Creole cattle: evidence of two independent continental sources

In order to clarify the historical origin and phylogeographic affinities of Creole cattle matrilineages throughout the American continent, we analysed published D-loop mtDNA sequences (n = 454) from Creole, Iberian and African cattle breeds. The Western European T3 haplogroup was the most common in American Creole cattle (63.6%), followed by the African T1 (32.4%) and the Near Eastern T2 haplogroups (4%). None of the sequences were found in Bos indicus types. Within the African T1 haplogroup there were two subclades, T1a and T1*, whose geographic distribution in America was clearly disjointed. T1a is a highly divergent clade originally reported for Creole cattle from Brazil and the Lesser Antilles, but whose geographic distribution in Africa remains unknown. In contrast, lineages attributable to T1* are restricted in America to the region colonized by the Spaniards. We propose a new hypothesis for the origins of Creole cattle that summarizes all previously published historical and genetic data. While the African T1* fraction in Creole cattle may have arrived in America through the Iberian breeds, the divergent T1a lineages may have been introduced by Portuguese and other European crowns from some unknown, not-yet-sampled African location. Additional molecular studies will be required for pinpointing the specific African regional source.

A simple method for domestic animal identification in Argentina using PCR-RFLP analysis of cytochrome b gene

We developed a simple, quick assay in order to discriminate forensic samples among human, and common domestic and livestock species of the Pampean region, Argentina. A mitochondrial cytochrome b fragment amplified with universal primers was separately digested with three restriction enzymes (AluI, HaeIII, and HinfI) and the resulting fragments were resolved through electrophoresis in polyacrylamide gels. This PCR-RFLP method allowed us to identify the target species and worked on degraded samples. The assay was successfully applied in livestock robbery cases in Argentine, and may be useful when attempting a first assessment as to the specific status of a forensic evidence.

Predominant African-derived mtDNA in Caribbean and Brazilian Creole cattle is also found in Spanish cattle (Bos taurus)

African-derived mitochondrial DNA (mtDNA) have been described in South American and Caribbean native cattle populations, which could have been introduced into America from Iberia or by direct importation from Africa. However, the similarity among described haplotypes is not known. We examined mtDNA variation in Guadeloupe Creole and Spanish cattle in an attempt to identify African-derived mtDNA haplotypes and compare them with those previously described. Eleven haplotypes clustered into the European taurine haplogroup (T3), two haplotypes into the African taurine (T1) haplogroup, and three haplotypes into the African-derived American haplogroup (AA). The AA1 and Eucons haplotypes were the most frequently observed. The presence of the AA haplogroup in Spanish cattle confirms historical records and genetic evidence of Iberian cattle as the main source of American native cattle origin. The possible origin of African-derived mitochondrial haplotypes in Iberian and Creole cattle is discussed, and the accumulated evidence does not support a founder effect from African ancestral cattle by direct importations. The presence of taurine AA and T3 haplotypes in Brazilian Nellore may indicate introgression by local European-derived cattle. Data presented in this work will contribute to the understanding of the origin of Guadeloupe Creole cattle.