Biodiversidade dos animais domésticos da Península Ibérica: uma perspetiva genómica 89 imputation to carry out population structure and conservation analyses at a lower cost (see text box). More importantly, generating high-quality genome assemblies for animals’ representative of native breeds will contribute significantly to avoid reference-allele bias, and allow for a better genetic characterization of more diverse and highly differentiated breeds from that of the reference genome (i.e., commercial breeds). For instance, it has recently been shown that a “pangenome” obtained from only five cattle (four breeds) and one yak genomes revealed more than 70 million bases that were not included in the Bos taurus reference genome (Crysnanto et al. 2021). Using complementary genomics and transcriptomics methods it should be possible to discover genes from non-reference sequences that are differentially expressed and thousands of variants that are not present in the reference genome. In our opinion, there is now great opportunity to develop interdisciplinary research among laboratories in the Iberian Peninsula to generate these genomes, identify the most appropriate methods to analyse the data and overcome the computational limitations to achieve these goals. Studies focused on questions related to breed genetic diversity and differentiation, or breed diversification, contributed key data for understanding these complex processes. However, integrating models of population structure to improve our understanding of the evolutionary processes that led to the diversification observed today is probably one of the greatest challenges facing population geneticists (Ajmone-Marsan et al. 2023). Combining the genomic data produced on several domesticated species with inferential approaches should provide very interesting and original avenues of research. 2. Investigating the domestication and breed differentiation processes Characterising agrobiodiversity using innovative approaches as described above will allow us to understand the processes of domestication and of breed diversification. The high biodiversity observed in domestic animals from the Iberian Peninsula can result from secondary domestication events and/ or high introgression from wild ancestors also very diverse in this territory. Understanding past adaptation to the local conditions and the modes of improvement of domesticated animals will also help us assess how biodiversity could adapt to future conditions (see section 3). 5 http://archaic.campus.ciencias.ulisboa.pt/ 6 https://aries.at.biopolis.pt/ 7 https://woofproject.wordpress.com/ The complex origin of Iberian primitive breeds is reflected in their high genetic diversity relative to that of their European counterparts, despite the large geographic distance of this territory from the presumed Near‐Eastern domestication center. This renders Iberian livestock a great example for investigating the genomic impact of the intricate processes of diversification regarding the last 200 years of specific breed formation and earlier admixture events. Multidisciplinary phylochronological approaches – merging zooarchaeology and genomics – are allowing us to capture ancestral genomic variation and to unveil origins, evolutionary trajectories and modes of improvement of Iberian livestock5,6,7. The co-evolution of several species (e.g., cattle, sheep and goats) is under analysis to cover a wide range of demographic processes and investigate post-domestication changes in inheritable traits (i.e., selection). It is not clear whether the high genetic diversity of well-adapted peripheral breeds derives from hybridization processes with contributions from wild ancestral species. Indeed, recently published analyses of autosomal genomes and mitogenomes obtained for four archaeological specimens of Iron Age (≈2,800 cal BP–2,000 cal BP) domestic cattle from the Eastern Maghreb (i.e., Althiburos, El Kef, Tunisia), corroborate the introgression of aurochs females into the domestic stock (Ginja et al. 2023). These first genomewide data of Iron Age cattle from the North-Eastern Maghreb re-open the discussion on whether there was a third domestication event of cattle in north Africa or if post-domestication hybridisation could explain the patterns of genetic variation detected. The greater genetic differentiation of West African taurine breeds such as N’Dama (longhorns) or Muturu (shorthorns) may-well derive from contributions of two distinct local aurochs populations. Diachronic archaeogenomics data from livestock across North Africa and Southern Europe are still lacking. Such information is needed to employ modelling approaches to reconstruct the demographic processes underlying breed differentiation. Answering these questions regarding the domestication process requires the development of methods and theoretical frameworks that integrate ancient population structure. 3. Studying the impact and resilience to climate change Identifying variants of adaptation to heat and drought in farm animals demands answering a key question on how genomic variation contributes to that of the phenotypes. One of the most compelling challenges of animal breeding and genetics has been to determine the genetic factors underlying com-
RkJQdWJsaXNoZXIy MTgxOTE4Nw==