Most Beefalo cattle have no detectable bison genetic ancestry

Authors: SHAPIRO, BETH - University Of California Santa Cruz; OPPENHEIMER, JONAS - University Of California Santa Cruz; Heaton, Michael; Kuhn, Kristen; GREEN, RICHARD - University Of California Santa Cruz; Blackburn, Harvey; Smith, Timothy

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 9/19/2024
Publication Date: 9/19/2024
Citation: Shapiro, B., Oppenheimer, J., Heaton, M.P., Kuhn, K.L., Green, R.E., Blackburn, H.D., Smith, T.P. 2024. Most Beefalo cattle have no detectable bison genetic ancestry. bioRxiv. https://doi.org/10.1101/2024.09.16.613218.
DOI: https://doi.org/10.1101/2024.09.16.613218

Interpretive Summary: Interbreeding is common among cattle species, often facilitated by human management to select for desirable traits. A prime example is the American Beefalo cattle breed, developed in the 1970s as a hybrid of American bison and domestic cattle. The American Beefalo Association typically requires a minimum of 3/8 bison, estimated from pedigree analysis, to be eligible for Beefalo classification. The bison ancestry in Beefalo was investigated at the molecular level by DNA sequencing to examine the mechanisms underlying hybridization between bison and domestic cattle, as part of a broader effort to understand the basis of speciation in the context of intermingling between emerging species. Sequence data from 50 historical and contemporary Beefalo animals revealed that most Beefalo did not contain detectable bison ancestry, although some exhibited lower levels of bison ancestry (2-18%). We also detected domestic zebu (humped) cattle ancestry in several Beefalo (2-38%), suggesting potential crossbreeding between domestic humped and non-humped cattle might contribute to the similar appearance between some Beefalo and bison. Our genetic analyses indicate that Beefalo and bison hybrids primarily resulted from repeated backcrossing to either pure bison or domestic cattle rather than breeding among hybrids, suggesting significant biological barriers to gene flow between bison and cattle. These findings call into question the 3/8 bison ancestry standard set by the Beefalo Association and highlight the value of genomic data in assessing claims of interspecies hybridization within the Bos genus

Technical Abstract: Hybridization is common among lineages in the genus Bos, often mediated through human management for the selection of adaptive or desirable traits. A recent example is the American Beefalo cattle breed, which was developed in the 1970s and defined as a hybrid between American bison (Bison bison) and cattle (Bos taurus). The American Beefalo Association typically require 3/8 bison ancestry to qualify as Beefalo. Here, we sought to characterize admixed ancestry among Beefalo as a component of a larger project to understand the role of hybridization in shaping present-day diversity in bison and cattle. We generated genomic data from 50 historical and present-day Beefalo and bison hybrids, including several important founding animals, as well as from 10 bison originating from commercial herds that represent potential sources of bison ancestry in Beefalo. We found that most Beefalo did not contain detectable bison ancestry. No individual Beefalo within our data set satisfies the ancestry requirements specified by the American Beefalo Association (ABA), although several Beefalo had smaller proportions of bison ancestry (2-18%). Some beefalo had detectable indicine cattle ancestry (2-38%), suggesting that hybridization of taurine and zebu cattle may contribute to morphological similarity between some Beefalo and bison. Overall, ancestry profiles of Beefalo and bison hybrid genomes are consistent with repeated backcrossing to either parental species rather than the breeding between hybrids themselves, implying significant barriers to gene flow between bison and cattle. Our results call into question the 3/8 bison ancestry targeted by the breed association and demonstrate the value of genomic information in examining claims of interspecies gene flow among Bos species.