Cattle demographic history modelled from autosomal sequence variation

The phylogeography of cattle genetic variants has been extensively described and has informed the history of domestication. However, there remains a dearth of demographic models inferred from such data. Here, we describe sequence diversity at 37 000 bp sampled from 17 genes in cattle from Africa, Europe and India. Clearly distinct population histories are suggested between Bos indicus and Bos taurus, with the former displaying higher diversity statistics. We compare the unfolded site frequency spectra in each to those simulated using a diffusion approximation method and build a best-fitting model of past demography. This implies an earlier, possibly glaciation-induced population bottleneck in B. taurus ancestry with a later, possibly domestication-associated demographic constriction in B. indicus. Strikingly, the modelled indicine history also requires a majority secondary admixture from the South Asian aurochs, indicating a complex, more diffuse domestication process. This perhaps involved multiple domestications and/or introgression from wild oxen to domestic herds; the latter is plausible from archaeological evidence of contemporaneous wild and domestic remains across different regions of South Asia.     

Could insecticide‐treated cattle reduce Afrotropical malaria transmission? Effects of deltamethrin‐treated Zebu on Anopheles arabiensis behaviour and survival in Ethiopia

Anopheles arabiensis Patton (Diptera: Culicidae) is the most widespread vector of malaria in the Afrotropical Region. Because An. arabiensis feeds readily on cattle as well as humans, the insecticide-treatment of cattle--as employed to control tsetse (Diptera: Glossinidae) and ticks (Acari: Ixodidae)--might simultaneously affect the malaria vectorial capacity of this mosquito. Therefore, we conducted field experiments in southern Ethiopia to establish whether Zebu cattle (Bos indicus L.) treated with a pour-on pyrethroid formulation of 1% deltamethrin, widely used to control ticks and tsetse, would be effective against An. arabiensis or cause the female mosquitoes to feed more frequently on humans, due to behavioural avoidance of insecticide-treated cattle. Contact bioassays (3 min exposure) showed that the insecticide remained effective for about 1 month (kill rate > 50%) against mosquitoes feeding on the flanks of treated cattle. A novel behavioural assay demonstrated that An. arabiensis readily fed on insecticide-treated cattle and were not deflected to human hosts in the presence of treated cattle. DNA-fingerprinting of bloodmeals revealed that An. arabiensis naturally feeds most frequently on older animals, consistent with the established practice of applying insecticide only to older cattle, while allowing younger untreated animals to gain immunity against infections transmitted by ticks. These encouraging results were tempered by finding that > 90% of An. arabiensis, An. pharoensis and An. tenebrosus females feed on the legs of cattle, farthest from the site of pour-on application along the animal's back and where the treatment may be least residual due to weathering. Observations of mosquitoes feeding naturally on insecticide-treated cattle showed that the majority of wild female anophelines alighted on the host animal for less than 1 min to feed, with significantly shorter mean duration of feeding bouts on insecticide-treated animals, and the effective life of the insecticide was only 1 week. Thus the monthly application of deltamethrin to cattle, typically used to control tsetse and ticks, is unlikely to be effective against An. arabiensis populations or their vectorial capacity. Even so, it seems likely that far greater impact on anopheline mosquitoes could be achieved by applying insecticide selectively to the legs of cattle.     

Cattle breed-variation in infestation by the horn fly Haematobia irritans

A study was carried out to assess the resistance of pure and cross-bred groups of cattle to the horn fly Haematobia irritans (Linnaeus) (Diptera: Muscidae) in northern Argentina. Pure-bred cattle were Criolla, Iberian Bos taurus Linnaeus (Artiodactyla: Bovidae) and Nellore, Bos indicus Linnaeus (Artiodactyla: Bovidae). Cross-bred cattle were Hereford, British B. taurus (34%) X Nellore (66%) and Hereford (66%) X Nellore (34%). All were heifers and animals were maintained in two groups, each containing a mixture of pure and cross-breeds. The lowest fly numbers were found on Criolla heifers and the highest on Hereford X Nellore cross-breeds. However, it could not be determined from this study whether this was a consequence of breed and/or size, as Criolla heifers were lighter than the corresponding Hereford X Nellore heifers. Fly numbers on the heifers followed an approximately negative binomial distribution. However, the ranking of individual animals in their level of infestation within subgroups was not consistent. Hence, culling the most infested heifers on any given date would at best give only a small improvement in H. irritans control.     

Boophilus microplus: the pattern of bovine immunoglobulin isotype responses to high and low tick infestations

Cattle present variable levels of resistance to ticks and the immune correlates of these heritable phenotypes must be known in order to develop effective vaccines. The antibody responses to tick salivary antigens were examined in cattle of tick-susceptible (Holstein) and tick-resistant (Nelore) breeds. After heavy infestations, levels of IgG1 and IgG2 antibodies decreased in Holsteins and remained the same in Nelores. Conversely, levels of IgE antibodies increased in Holsteins. Different sizes of tick burdens modulated the IgG1 antibody response in a susceptible breed (Aberdeen): levels were higher than in controls in heavily infested animals, but not in those undergoing intermediary or minimal infestations. The three experimental groups presented similar levels of IgG2 antibodies. Levels of IgE antibodies were higher only in animals undergoing intermediate infestations. These results indicate that tick infestations suppress the IgG antibody response in susceptible breeds, that IgE antibodies are not protective, and that the dose of tick saliva modulates the isotype of host antibody responses.     

Serum albumin polymorphism and its relationship to economic traits in crossbred cattle

The serum albumin genotypes of 65 Jersey × Hariana (F₁), 75 Holstein Friesian × Hariana (F₁) and 47 Brown Swiss × Hariana (F₁) crossbred cows were determined by starch gel electrophoresis. Two albumin alleles Alb^F and Alb^s , but only either as Alb^F homozygotes or Alb^Fs heterozygotes, were observed amongst these animals. There were no Alb^S homozygotes or other genotypes. Highly significant relationships between albumin genotypes and both birth weights and first-lactation milk yields of these cows were observed. The Alb^F allele was associated with increased milk yield and greater birth weights.     

Bos indicus introgression into (peri‐)alpine cattle breeds – evidence from the analysis of bovine whey protein variants

The major bovine whey proteins, α‐lactalbumin (α‐LA) and β‐lactoglobulin (β‐LG), exhibit breed‐specific genetic variation. The aim of this study was to identify possible new protein variants and determine the distribution of variants across a variety of 18 taurine and indicine cattle breeds applying a DNA‐based sequencing approach. To this end, the open reading frames of the respective genes (LALBA and LGB) were sequenced in 476 animals. Within the LALBA gene, a previously unknown synonymous and a previously undesignated non‐synonymous nucleotide exchange were identified. Furthermore, two known α‐LA variants (A and B) and four known β‐LG variants (A, B, C and W) were determined. The occurrence of typical indicine variants in some taurine cattle breeds, such as Suisse Eringer, German Hinterwälder and Hungarian Grey Steppe, further supports the hypothesis of ancient Bos indicus introgression into (peri‐)alpine cattle breeds.     

Beta‐globin gene evolution in the ruminants: evidence for an ancient origin of sheep haplotype B

Domestic sheep (Ovis aries) can be divided into two groups with significantly different responses to hypoxic environments, determined by two allelic beta‐globin haplotypes. Haplotype A is very similar to the goat beta‐globin locus, whereas haplotype B has a deletion spanning four globin genes, including beta‐C globin, which encodes a globin with high oxygen affinity. We surveyed the beta‐globin locus using resequencing data from 70 domestic sheep from 42 worldwide breeds and three Ovis canadensis and two Ovis dalli individuals. Haplotype B has an allele frequency of 71.4% in O. aries and was homozygous (BB) in all five wild sheep. This shared ancestry indicates haplotype B is at least 2–3 million years old. Approximately 40 kb of the sequence flanking the ~37‐kb haplotype B deletion had unexpectedly low identity between haplotypes A and B. Phylogenetic analysis showed that the divergent region of sheep haplotype B is remarkably distinct from the beta‐globin loci in goat and cattle but still groups with the Ruminantia. We hypothesize that this divergent ~40‐kb region in haplotype B may be from an unknown ancestral ruminant and was maintained in the lineage to O. aries, but not other Bovidae, evolving independently of haplotype A. Alternatively, the ~40‐kb sequence in haplotype B was more recently acquired by an ancestor of sheep from an unknown non‐Bovidae ruminant, replacing part of haplotype A. Haplotype B has a lower nucleotide diversity than does haplotype A, suggesting a recent bottleneck, whereas the higher frequency of haplotype B suggests a subsequent spread through the global population of O. aries.     

Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping

Background

Natural selection has molded evolution across all taxa. At an arguable date of around 330,000 years ago there were already at least two different types of cattle that became ancestors of nearly all modern cattle, the Bos taurus taurus more adapted to temperate climates and the tropically adapted Bos taurus indicus. After domestication, human selection exponentially intensified these differences. To better understand the genetic differences between these subspecies and detect genomic regions potentially under divergent selection, animals from the International Bovine HapMap Experiment were genotyped for over 770,000 SNP across the genome and compared using smoothed F_ST. The taurine sample was represented by ten breeds and the contrasting zebu cohort by three breeds.

Results

Each cattle group evidenced similar numbers of polymorphic markers well distributed across the genome. Principal components analyses and unsupervised clustering confirmed the well-characterized main division of domestic cattle. The top 1% smoothed F_ST, potentially associated to positive selection, contained 48 genomic regions across 17 chromosomes. Nearly half of the top F_ST signals (n = 22) were previously detected using a lower density SNP assay. Amongst the strongest signals were the BTA7:~50 Mb and BTA14:~25 Mb; both regions harboring candidate genes and different patterns of linkage disequilibrium that potentially represent intrinsic differences between cattle types. The bottom 1% of the smoothed F_ST values, potentially associated to balancing selection, included 24 regions across 13 chromosomes. These regions often overlap with copy number variants, including the highly variable region at BTA23:~24 Mb that harbors a large number of MHC genes. Under these regions, 318 unique Ensembl genes are annotated with a significant overrepresentation of immune related pathways.

Conclusions

Genomic regions that are potentially linked to purifying or balancing selection processes in domestic cattle were identified. These regions are of particular interest to understand the natural and human selective pressures to which these subspecies were exposed to and how the genetic background of these populations evolved in response to environmental challenges and human manipulation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-14-876) contains supplementary material, which is available to authorized users.     

Late Triassic and Lower Jurassic Foraminifera of the carbonate platform of the Beyaz Aladağ Group (Eastern Taurus,Turkey): New stratigraphic implications

Foraminifera have proven to be reliable biostratigraphic indicators. Accordingly, Triassic and Early Jurassic benthic Foraminifera allow us to define a biostratigraphic zonation within the carbonate platform of Kayseri (Yahyal?), Göksun (Kahramanmara?) and Sivas (Delikta?) regions in the Eastern Taurus (Ceviz, Alada?, Kaman and Felfan Mountains). Seven new stratigraphic sections are described in detail and the first precise inventory and illustration of the benthic foraminifer assemblages from the Triassic successions are presented over a large geographic area. The stratigraphic and palaeontological features of the Lower Mesozoic carbonate units of these mountains include several synchronous transgressive–regressive events that suggest continuity of the Lower Mesozoic environments over a large parautochthonous Taurus zone. Palaeogeographic considerations about the Eastern Taurus carbonates are given, evidencing three stages of development underwent by the studied area: 1) a stable continental margin from Lower Triassic to Lower Cretaceous; 2) a dismantling of the continental margin and first emplacement of ophiolites in the Upper Cretaceous; and 3) a deformation of the continental margin and emplacement of the Peridotite Nappe in the uppermost Cretaceous (Maastrichtian).     

Performance,carcass characteristics and meat quality of Nellore cattle supplemented with supranutritional doses of sodium selenite or selenium-enriched yeast

The enrichment of meat with selenium is important to improve the intake of selenium by humans. The effects of supranutritional doses of sodium selenite or selenium-enriched yeast on performance, carcass characteristics and meat quality were evaluated using 63 Nellore cattle in a completely randomized design with two sources (sodium selenite and selenium-enriched yeast), three levels (0.3, 0.9 and 2.7 mg Se/kg DM) and control treatment (without addition of selenium). Final body weight (BW), average daily gain, dry matter intake and gain to feed ratio (G : F) at the end of 84 days of supplementation were not influenced by treatments (P>0.05). Values of pH, ribeye area, back fat thickness and marbling score were also not influenced by treatments (P>0.05). Dressing percentage was greater (P=0.02) in Nellore cattle supplemented with organic Se (58.70%) compared to animals supplemented with inorganic Se (57.94%). Hot carcass weight increased (P=0.05) with the increasing of Se levels in the diet. Colour, shear force (SF), cooking and drip loss remained unchanged (P>0.05); however thiobarbituric acid reactive substances was 15.51% higher with inorganic Se compared with organic Se. The selenium concentration in the meat of animals receiving organic selenium was higher (P<0.001) than that of animals receiving sodium selenite, at all levels (0.3; 0.9 and 2.7 mg/kg DM). The meat of animals receiving 2.7 mg of organic Se/kg of DM presented concentration of 372.7 μg Se/kg in the L.dorsi muscle, and the intake of 150 g of this meat by humans provides approximately 100% of the recommended Se intake (55 μg Se/day for adults). Therefore, the use of supranutritional doses of 2.7 mg Se/kg of DM, regardless of source, is a way of naturally producing selenium-enriched meat without compromising performance, carcass characteristics and quality of Nellore bovine meat.