Most Beefalo cattle have no detectable bison genetic ancestry

Reviewer #1 (Public review):

Summary:

This study used whole genome data to investigate Beefalo ancestry for the first time, filling the gap in the field of Beefalo ancestry. The authors used preserved semen samples to generate genomic data on 47 registered Beefalo and 3 bison hybrids, further questioning the ABA's stated goal of ⅜ bison ancestry. In addition, the authors also show that ancestry profiles of Beefalo and bison hybrid genomes are consistent with repeated backcrossing to either parental species, demonstrating the value of genomic information in examining gene flow between species in the genus Bison. This is an interesting study that still has some major weaknesses that exist, but overall, the work demonstrates the utility of genomic information in validating specific breeding claims for a more complete understanding of gene flow and genetic variation among bovine species.

Strengths:

Numerous genetic analysis methods such as PCA, ADMIXTURE, F4 ratios, and local ancestry inference techniques revealed that no single Beefalo set meets the ancestry requirements set by the American Beefalo Association (ABA) and some beefalo had detectable indicine cattle ancestry.

Weaknesses:

While this study contributes to our knowledge of Beefalo ancestry, there are some key issues that need to be addressed in terms of analysing the specific results as well as writing the article.

Reviewer #2 (Public review):

Summary:

Shapiro et al. set out to verify the American Beefalo Association's claim that Beefalo cattle possess 37.5% bison ancestry. They employ a comprehensive range of well-established population genomics methods to estimate ancestry in these hybrid populations, including PCA, ADMIXTURE, D and F statistics, and local ancestry inference. Their findings conclusively demonstrate that most Beefalo lack the claimed bison ancestry, with only 8 out of 47 samples showing any detectable bison ancestry, ranging from 2 - 18%.

Strengths:

The primary strength of this analysis lies in the comprehensive dataset available to the authors, which includes important foundational Beefalo individuals and various reference populations. The rigorous and multi-faceted methodological approach employs several well-established techniques in population genomics for detecting and measuring admixture. Each method used has a firm basis in the field, providing consistent and robust results. The authors' approach of using PCA to initially assess the data within a global context, followed by more specific analyses using ADMIXTURE and D-statistics, provides a clear and logical progression of evidence. The presentation of these results in figures is particularly effective, clearly illustrating the key findings of the study. Additionally, the examination of both autosomal and sex chromosome ancestry offers a more complete understanding of Beefalo genetic composition and the mechanics of bison-cattle hybridisation.

Weaknesses:

One limitation of this analysis is the relatively low coverage (~2x) of many Beefalo samples. However, the authors have taken steps to mitigate biases that may arise from this. Another weakness is the limited sampling of contemporary Beefalo populations, as the study focuses primarily on historical samples. This may limit our understanding of how Beefalo genetics may have changed over time.

Appraisal:

The authors have clearly achieved their primary aim using a rigorous and comprehensive methodology. Their extensive dataset and multi-faceted analytical approach provide strong support for their conclusions. The study not only addresses its main research question but also reveals unexpected insights into Beefalo genetics, particularly the presence of zebu ancestry.

Discussion:

This study is valuable for several reasons beyond its primary findings. First, it definitively addresses and refutes the claim of 37.5% bison ancestry in Beefalo, providing crucial information for those studying these interspecies hybrids and the viability of their offspring. Second, it reveals the unexpected presence of zebu ancestry in many Beefalo, raising intriguing questions about the breed's development and the potential role of zebu cattle in achieving desired traits. This finding suggests that the distinctive appearance of Beefalo may be due in part to zebu admixture rather than bison ancestry. Third, the study highlights the significant barriers to admixture between bison and cattle, both in controlled breeding programs and potentially in wild populations. This has important implications for conservation genetics and our understanding of gene flow between these species. Lastly, the study demonstrates the power of genomic analysis in verifying breed claims and understanding the complex history of domestic animal breeds. These findings open new avenues for research in bovine genomics, breed development, and the dynamics of interspecies hybridisation.

Reviewer #3 (Public review):

Summary:

I really like this topic and study. But I think much can be more focused and tightened up. All the components are here - just some more refining to really make the storyline clear, the journey of discovery, and the impact of such knowledge.

Strengths:

The authors dive directly into the question of genomic ancestry as compared to the breed club's reported ancestry with heavy, quantitative data and critical analytical methods. The questioning line is direct and does not meander. The reader learns about the challenges of breeding associations, and values of understood ancestry, and presents a clear need of re-evaluating the breed standards and expectations of beefalo (if ancestry is indeed the primary goal instead of a phenotype-driven breed mission).

Weaknesses:

Much of the quantitative results are only referred to in the main text with qualitative language. Please incorporate more written quantitative results to highlight evidence that underlines the study narrative because it is quite an interesting study!