Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.

The domestication of livestock represented a crucial step in human history. By using endogenous retroviruses as genetic markers, we found that sheep differentiated on the basis of their “retrotype” and morphological traits, dispersed across Eurasia and Africa via separate migratory episodes. Relicts of the first migrations include the Mouflon, as well as breeds previously recognized as “primitive” on the basis of their morphology, such as the Orkney, Soay and the Nordic short-tailed sheep now confined to the periphery of NW Europe. A later migratory episode, involving sheep with improved production traits, shaped the vast majority of present-day breeds. The ability to differentiate genetically primitive sheep from more modern breeds provides valuable insights into the history of sheep domestication.

Blood samples were collected from 743 animals from 15 indigenous, 2 old imported, and 3 commercial North European cattle breeds. The samples were analyzed for 11 erythrocyte antigen systems, 8 proteins, and 10 microsatellites, and used to assess inter- and intrabreed genetic variation and genetic population structures. The microsatellites BoLA-DRBP1 and CSSM66 were nonneutral markers according to the Ewens-Watterson test, suggesting some kind of selection imposed on these loci. North European cattle breeds displayed generally similar levels of multilocus heterozygosity and allelic diversity. However, allelic diversity has been reduced in several breeds, which was explained by limited effective population sizes over the course of man-directed breed development and demographic bottlenecks of indigenous breeds. A tree showing genetic relationships between breeds was constructed from a matrix of random drift-based genetic distance estimates. The breeds were classified on the basis of the tree topology into four major breed groups, defined as Northern indigenous breeds, Southern breeds, Ayrshire and Friesian breeds, and Jersey. Grouping of Nordic breeds was supported by documented breed history and geographical divisions of native breeding regions of indigenous cattle. Divergence estimates between Icelandic cattle and indigenous breeds suggested a separation time of more than 1,000 years between Icelandic cattle and Norwegian native breeds, a finding consistent with historical evidence.

Recent discoveries that high prolificacy in sheep carrying the Booroola gene (FecB) is the result of a mutation in the BMPIB receptor and high prolificacy in Inverdale sheep (FecX(I)) is the result of a mutation in the BMP15 oocyte-derived growth factor gene have allowed direct marker tests to be developed for FecB and FecX(I). These tests were carried out in seven strains of sheep (Javanese, Thoka, Woodlands, Olkuska, Lacaune, Belclare, and Cambridge) in which inheritance patterns have suggested the presence of major genes affecting prolificacy and in the prolific Garole sheep of India, which have been proposed as the ancestor of Australian Booroola Merinos. The FecB mutation was found in the Garole and Javanese sheep but not in Thoka, Woodlands, Olkuska, Lacaune, Belclare, and Cambridge sheep. None of the sheep tested had the FecX(I) mutation. These findings present strong evidence to support historical records that the Booroola gene was introduced into Australian flocks from Garole (Bengal) sheep in the late 18th century. It is unknown whether Javanese Thin-tailed sheep acquired the Booroola gene directly from Garole sheep from India or via Merinos from Australia. The DNA mutation test for FecB will enable breeding plans to be developed that allow the most effective use of this gene in Garole and Javanese Thin-tailed sheep and their crosses.

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Population contribution to genetic diversity can be estimated using neutral variation. However, population expansion or hybridization of diverged ancestries may weaken correlation between neutral and non-neutral variation. Microsatellite variation was studied at 25 loci in 20 native and 12 modern or imported northern European sheep breeds. Breed contributions to total gene diversity, allelic richness and mean allele-sharing distance between individuals were measured. Indications of changes in population size and admixtures of divergent ancestries were investigated and the extent of inbreeding was estimated. The northern European sheep demonstrated signs of reduction in effective population size. Many old, small populations made a substantial positive contribution to total molecular variation, but populations with several divergent major ancestries did not contribute substantially to molecular variation, with the exception of the Norwegian Rygja sheep. However, several diverged major ancestries may cause it to contribute less to non-neutral variation than expected from the microsatellite data. Breed uniqueness and within-breed variability generally had opposite effects on breed contributions to molecular diversity. The degree of inbreeding did not reflect the breed contribution to total gene diversity or allelic richness, but inbred populations increased the mean allele-sharing distance between individuals. Our study indicates breed conservation to be especially important in maintaining allelic variation in northern European sheep and supports the evolutionary importance of peripheral populations.

Allele frequencies at four milk protein loci were studied in five modern and 17 old Nordic cattle breeds in order to reveal variants that are characteristic for these populations. The B allele of CSN3, which has been associated with improved manufacturing properties of milk, showed significantly lower frequencies in modern production breeds than in old breeds of interest for conservation purposes. Characteristic frequencies of CSN1S1 (C), CSN2 (A2) and CSN3 (B) were found in Icelandic cattle, Swedish Mountain cattle, Northern Finncattle and Western Fjord cattle, which indicate a common origin of these populations. Further comparisons of allele frequencies in old Nordic breeds suggest sorting of these breeds into two groups with a northern and southern geographic location.

Studies of domestic animals are performed on breeds, but a breed does not necessarily equate to a genetically defined population. The division of sheep from three native and four modern Baltic sheep breeds was studied using 21 microsatellite loci and applying a Bayesian clustering method. A traditional breed-wise approach was compared to that relying on the pattern of molecular diversity. In this study, a breed was found to be inconsistent with a distinct genetic population for three reasons: (i) a lack of differentiation between modern Baltic breeds, since the majority of the studied sheep formed a single population; (ii) the presence of individuals of foreign ancestry within the breed; and (iii) an undefined local Saaremaa sheep was referred to as a breed, but was shown to consist of separate populations. In the breed-wise approach, only the clearly distinct Ruhnu sheep demonstrated low within-breed variation, although the newly identified Saaremaa populations also have low variability. Providing adequate management recommendations for the Saaremaa sheep is not possible without further studies, but the potential harmful effects of inbreeding in the Ruhnu sheep could be reduced through the use of two genetically related Saaremaa populations. In other breeds, excessive crossing appears to be a larger concern than inbreeding. Assigning individuals into populations based on the pattern of genetic diversity offers potentially unbiased means of elucidating the genetic population structure of species. Combining these genetic populations with phenotypic and aetiological data will enable formulation of the most informed recommendations for gene resource management. Heredity (2005) 94, 448-456.