Genetic variation within livestock populations underpins global food security, resilience, and the long-term sustainability of breeding programs. Despite its fundamental role, harmonized approaches for assessing and monitoring genetic variation across data sources remain limited. This review provides an integrated framework for assessing genetic variation in livestock using demographic, pedigree, and genomic data, developed by FAO experts and international collaborators. Demographic indicators offer essential insight into population size, sex ratio, and reproductive structure, while pedigree data allow detailed evaluation of genetic relatedness, inbreeding, and effective population size (Ne) over time. Genomic information now provides unprecedented accuracy in characterizing allelic variation, population structure with admixture, and the dynamics of inbreeding and drift. Each data source differs in availability, resolution, and interpretive limits; therefore, complementary use of demographic, pedigree, and genomic measures is recommended for effective monitoring and decision-making. This framework outlines the main properties, applications, and constraints of these approaches and provides guidance on selecting appropriate indicators for monitoring genetic variation within and among livestock populations. Its implementation supports the objectives of the Global Plan of Action for Animal Genetic Resources and the Kunming-Montreal Global Biodiversity Framework, contributing to evidence-based management of livestock diversity worldwide.

ABSTRACT Historically, the eastern Italian Alps have provided crucial geographic corridors for cultural and genetic exchange between the Mediterranean region and Central and Northern Europe. Although recent archaeogenomic data suggest a strong regional persistence of Anatolian Neolithic ancestry followed by the arrival of Yamnaya-related components during the Bronze Age, the genomic landscape of modern Alpine populations remains largely unmapped. In this study, we verified the persistence of these signals in the present-day Rendena and Ledro Valleys by integrating novel complete mitochondrial genomes (N=185) and genome-wide SNP data (N=96), the latter combined with a novel Italian genomic dataset (N=139). Our findings show that the Rendena and Ledro populations form a distinct “modern Alpine” genomic group, which retains a significant proportion of early European Neolithic ancestry, aligning with ancient eastern Italian Alpine individuals and modern Sardinians. More recently, geographic isolation and localized genetic drift appear to have shaped the two valleys differently. Demographic reconstructions reveal asynchronous population declines over the past two millennia, followed by a sharp, synchronized bottleneck 200-300 years ago, which coincided with historical plague outbreaks. Remarkably, this structured drift persisted at an extremely fine microgeographic scale within the valleys, resulting in internal genetic subclusters that directly correlate with local topography. This micro-differentiation was likely maintained by steep geographic barriers and/or local endogamous practices. This study ultimately underscores how geographic barriers and isolation can preserve ancient genomic components and shape highly localized genetic structures over centuries even to the modern day.

Val Rendena, an isolated Alpine valley in northern Italy, is home to an autochthonous, dual-purpose cattle breed with unique historical and morphological traits, which has been preserved by local breeders despite severe epidemics since the 1700s. While previous genome-wide studies identified signatures of selection in Rendena cattle, little is known about its evolutionary history. To address this issue, we analyzed complete mitogenomes from 137 Rendena individuals, selected to represent the majority of maternal lineages across the breed, as well as mitogenomes from 31 Alpine Grey individuals, purportedly closely related to Rendena cattle. We identified 86 distinct mitochondrial DNA (mtDNA) haplotypes in the Rendena breed, indicating a high haplotype diversity (Hd = 0.986). Phylogenetic analyses revealed that virtually all samples belong to the T macro-haplogroup (T3 = 91

Goats were among the earliest managed animals, making them a natural model to explore the genetic consequences of domestication. However, a challenge in ancient genomic analysis is the relatively low genome coverage for most samples, limiting analysis to pseudohaploid genotypes. Genotype imputation offers potential to alleviate this limitation by improving information content and accuracy in low coverage genomes. To test this, we used published high coverage (>8✕) goat palaeogenomes, imputing downsampled genomes using the VarGoats dataset (1,372 individuals) as a reference panel. Measuring concordance between imputed and high coverage genotypes, we find high concordance after filtering for common (>5%), high confidence variants, with 0.5✕ genomes reaching >0.97 concordance. There is a trade-off between coverage, genotype probability (GP) thresholds, and genotype recovery, where higher coverage and more lenient GP thresholds result in higher recovery, and a reduction in heterozygous false-positive rates with stricter thresholds. We then imputed 36 goat palaeogenomes with ≥0.5✕ coverage to examine runs-of-homozygosity (ROH) and identity-by-descent (IBD) patterns. Using a novel approach combining ROH profiles across tools, we find that among Neolithic goats, ROH increases with distance from the Zagros Mountains, suggesting a large effect of the initial dispersal of managed herds. Inbreeding levels decrease across Southwest Asia in more recent periods. IBD mirrored this pattern, with less relatedness in the early herding site of Ganj Dareh compared to higher relatedness in goats from later in the dispersal process. These findings provide insights into the genetic consequences of early goat management on demography, and confirm the utility of imputation in leveraging low coverage palaeogenomes.

Effective population size (Ne) is a key parameter in various biological disciplines, including evolutionary biology, conservation genetics, and livestock breeding programs. When applying genomic approaches to estimate Ne or other indicators of genetic variation, sample size is among the critical factors that directly affect the balance between cost and precision. In this study, we investigated the impact of sample size on Ne estimates by analyzing data from previous genotyping studies and simulations. Our results suggest that a sample size of 50 animals is a reasonable approximation of the “true” (“unbiased”) Ne value within the populations analyzed. While estimating the Ne value is an important starting point in population genetics, additional factors, such as the degree of inbreeding, population structure, and admixture, must be taken into account to obtain a comprehensive genetic evaluation and avoid misinterpretation. We conclude that linkage disequilibrium (LD)-based approaches are well suited for the estimation of Ne in livestock populations. However, careful interpretation of results is essential as current bioinformatics tools may introduce potential biases due to methodological assumptions, marker density, or population-specific factors.

Technological advancements and decrease of costs of whole-genome sequencing approaches has made available a huge and ever increasing amount of resequencing data for many species. It is thus now possible to assemble large sized datasets encompassing the molecular variation of several species and/or populations or breeds. Nonetheless, these datasets can be extremely variable in terms of geographical provenance and sample sizes, with taxonomic groups varying from hundreds to just a few or even one single entry. In such circumstances, the application of standard filtering approaches may lead to the introduction of biases and to the under/over representation of some groups or gene pools. Commonly adopted variant filtering approaches relying on Minor Allele Frequency (MAF) and Linkage Disequilibrium (LD) may not be suitable to treat datasets representing broadscale diversity of multiple species, due to remarkable differences in LD structure and in the frequency of variants at the local vs. global scale. Thus, by exploiting the VarGoats 1000 goat genome project data as an optimal case study, we devised a novel approach based on within-population subsampling, Minor Allele Count (MAC) and marker spacing (bp-space), specifically designed to avoid biases introduced by standard filtering procedures and to adequately represent continental and species-specific variation. Starting from a quality-filtered dataset of >28M SNPs from 1372 animals, we obtained a dataset of <14M markers and 750 individuals, complying with the initial requirements and more handy for further computational steps. The dataset was validated by PCA, Neighbor Joining and Admixture analyses. ### Competing Interest Statement The authors have declared no competing interest.

Background MicroRNAs (miRNAs) are a type of small non-coding RNAs involved in the post-transcriptional repression of target mRNA transcripts, and responsible for the fine-tuning of numerous molecular mechanisms regulating cell metabolism. In goats, multiple miRNAs are involved in coordinating the expression of networks of genes with key roles on the phenotypic variation of milk and meat traits. Although a comprehensive set of goat miRNAs has been annotated, their levels of polymorphism have not been characterized yet. Such information would be relevant in order to explore the effects of miRNA variants on phenotypes of economic interest in goats. Results By using whole-genome sequencing data from 770 domestic goats with African, Asian, and European origins, we have identified polymorphic sites located within miRNA genes as well as in their flanking regions. In doing so, we have found that miRNA polymorphisms are rare (median alternative allele frequency of 0.46%) and that the distribution of polymorphic sites within and around miRNA loci is uneven. Remarkably, the stem, loop and neighbouring regulatory regions of precursor miRNA hairpins show a significantly higher polymorphism density compared to the miRNA seed, which determines the binding affinity to target mRNAs. Moreover, we have detected a differential segregation of miRNA variants across and within continental regions, with an enriched segregation of putatively high impact polymorphisms, i.e. those located in the seed and other biologically relevant regions of miRNA genes, in isolated goat populations with a low census and elevated content of runs of homozygosity. Conclusion Goat miRNA genes display low levels of variation particularly in the seed region, likely due to the action of strong purifying selection removing mutations with potential effects on gene regulatory networks linked to miRNA function. Moreover, miRNA polymorphisms tend to be more abundant in goat breeds with high levels of homozygosity, likely because purifying selection is less efficient in populations of limited size. The information provided in the current work could be useful to identify miRNA polymorphisms contributing to phenotypic variation through the disruption of gene regulatory networks in domestic goats, as well as to assess their potential impact on adaptation and fitness. ### Competing Interest Statement The authors have declared no competing interest.

The origin of Arctic charr populations in the lakes of the Italian Alps is not well understood. While some studies have suggested that they are postglacial relics, others have proposed that these populations are the result of intentional stocking efforts dating back to the sixteenth century. Subsequent introductions of Arctic charr to these lakes have made it difficult to untangle the evolutionary history of these Alpine populations. In this study, we examined the distribution of genetic variation among Arctic charr collected throughout their Northern and Southern European ranges at the beginning of the twenty-first century, using nuclear (amplified fragment length polymorphisms) and mitochondrial (control region and cytochrome oxidase I) loci. These analyses revealed the impact of restocking activities, which have resulted in admixture and hybridisation with Brook charr (Salvelinus fontinalis) in Italian alpine lakes and provides clues on the native or pseudo-native origin of Trentino-Alto Adige populations. The lack of detailed historical information, however, makes it difficult to disentangle the postglacial history of the species and to determine how much of the current diversity pattern can be ascribed to the consequences of Pleistocene events or anthropogenic activities.

Animal husbandry is one of man's oldest occupations. It began with the domestication of animals and developed continuously, in parallel with the evolution of human society. The selection and improvement of goats in Romania was not a clearly defined objective until around 1980. In recent years, with the increasing economic value given to goats, breeding programs are becoming established. In Romania, a few goat genetic studies using microsatellites and mtDNA have been carried out; however, a systematic characterization of the country's goat genomic resources remains missing. In this study, we analyzed the genetic variability of Carpatina goats from four distinct geographical areas (northern, north-eastern, eastern and southern Romania), using the Illumina OvineSNP60 (RefSeq ARS1) high-density chip for 67 goats. Heterozygosity values, inbreeding coefficients and effective population size across all autosomes were calculated for those populations that inhabit high- and low-altitude and high- and low-temperature environments. Diversity, as measured by expected heterozygosity (HE), ranged from 0.413 in the group from a low-temperature environment to 0.420 in the group from a high-temperature environment. Within studied groups, the HT (high temperature) goats were the only group with a positive but low average inbreeding coefficient value, which was 0.009. After quality control (QC) analysis, 46,965 SNPs remained for analysis (MAF < 0.01). LD was calculated for each chromosome separately. The Ne has been declining since the time of domestication, having recently reached 123, 125, 185 and 92 for the HA (high altitude), LA (low altitude), HT (high temperature) and LT (low temperature) group, respectively. Our study revealed a low impact of inbreeding in the Carpatina population, and the Ne trend also indicated a steep decline in the last hundred years. These results will contribute to the genetic improvement of the Carpatina breed.

In Apis mellifera, csd is the primary gene involved in sex determination: haploid hemizygous eggs develop as drones, while females develop from eggs heterozygous for the csd gene. If diploid eggs are homozygous for the csd gene, diploid drones will develop, but will be eaten by worker bees before they are born. Therefore, high csd allelic diversity is a priority for colony survival and breeding. This study aims to investigate the variability of the hypervariable region (HVR) of the csd gene in bees sampled in an apiary under a selection scheme. To this end, an existing dataset of 100 whole-genome sequences was analyzed with a validated pipeline based on de novo assembly of sequences within the HVR region. In total, 102 allelic sequences were reconstructed and translated into amino acid sequences. Among these, 47 different alleles were identified, 44 of which had previously been observed, while 3 are novel alleles. The results show a high variability in the csd region in this breeding population of honeybees.

Given the multitude of challenges Earth is facing, sustainability science is of key importance to our continued existence. Evolution is the fundamental biological process underlying the origin of all biodiversity. This phylogenetic diversity fosters the resilience of ecosystems to environmental change, and provides numerous resources to society, and options for the future. Genetic diversity within species is also key to the ability of populations to evolve and adapt to environmental change. Yet, the value of evolutionary processes and the consequences of their impairment have not generally been considered in sustainability research. We argue that biological evolution is important for sustainability and that the concepts, theory, data, and methodological approaches used in evolutionary biology can, in crucial ways, contribute to achieving the UN Sustainable Development Goals (SDGs). We discuss how evolutionary principles are relevant to understanding, maintaining, and improving Nature Contributions to People (NCP) and how they contribute to the SDGs. We highlight specific applications of evolution, evolutionary theory, and evolutionary biology's diverse toolbox, grouped into four major routes through which evolution and evolutionary insights can impact sustainability. We argue that information on both within-species evolutionary potential and among-species phylogenetic diversity is necessary to predict population, community, and ecosystem responses to global change and to make informed decisions on sustainable production, health, and well-being. We provide examples of how evolutionary insights and the tools developed by evolutionary biology can not only inspire and enhance progress on the trajectory to sustainability, but also highlight some obstacles that hitherto seem to have impeded an efficient uptake of evolutionary insights in sustainability research and actions to sustain SDGs. We call for enhanced collaboration between sustainability science and evolutionary biology to understand how integrating these disciplines can help achieve the sustainable future envisioned by the UN SDGs.

Abstract Background Rendena is a dual-purpose cattle breed, which is primarily found in the Italian Alps and the eastern areas of the Po valley, and recognized for its longevity, fertility, disease resistance and adaptability to steep Alpine pastures. It is categorized as 'vulnerable to extinction' with only 6057 registered animals in 2022, yet no comprehensive analyses of its molecular diversity have been performed to date. The aim of this study was to analyse the origin, genetic diversity, and genomic signatures of selection in Rendena cattle using data from samples collected in 2000 and 2018, and shed light on the breed's evolution and conservation needs. Results Genetic analysis revealed that the Rendena breed shares genetic components with various Alpine and Po valley breeds, with a marked genetic proximity to the Original Braunvieh breed, reflecting historical restocking efforts across the region. The breed shows signatures of selection related to both milk and meat production, environmental adaptation and immune response, the latter being possibly the result of multiple rinderpest epidemics that swept across the Alps in the eighteenth century. An analysis of the Rendena cattle population spanning 18 years showed an increase in the mean level of inbreeding over time, which is confirmed by the mean number of runs of homozygosity per individual, which was larger in the 2018 sample. Conclusions The Rendena breed, while sharing a common origin with Brown Swiss, has developed distinct traits that enable it to thrive in the Alpine environment and make it highly valued by local farmers. Preserving these adaptive features is essential, not only for maintaining genetic diversity and enhancing the ability of this traditional animal husbandry to adapt to changing environments, but also for guaranteeing the resilience and sustainability of both this livestock system and the livelihoods within the Rendena valley.

Donkeys (Equus asinus) have been used extensively in agriculture and transportations since their domestication, ca. 5000-7000 years ago, but the increased mechanization of the last century has largely spoiled their role as burden animals, particularly in developed countries. Consequently, donkey breeds and population sizes have been declining for decades, and the diversity contributed by autochthonous gene pools has been eroded. Here, we examined coding-region data extracted from 164 complete mitogenomes and 1392 donkey mitochondrial DNA (mtDNA) control-region sequences to (i) assess worldwide diversity, (ii) evaluate geographical patterns of variation, and (iii) provide a new nomenclature of mtDNA haplogroups. The topology of the Maximum Parsimony tree confirmed the two previously identified major clades, i.e. Clades 1 and 2, but also highlighted the occurrence of a deep-diverging lineage within Clade 2 that left a marginal trace in modern donkeys. Thanks to the identification of stable and highly diagnostic coding-region mutational motifs, the two lineages were renamed as haplogroup A and haplogroup B, respectively, to harmonize clade nomenclature with the standard currently adopted for other livestock species. Control-region diversity and population expansion metrics varied considerably between geographical areas but confirmed North-eastern Africa as the likely domestication center. The patterns of geographical distribution of variation analyzed through phylogenetic networks and AMOVA confirmed the co-occurrence of both haplogroups in all sampled populations, while differences at the regional level point to the joint effects of demography, past human migrations and trade following the spread of donkeys out of the domestication center. Despite the strong decline that donkey populations have undergone for decades in many areas of the world, the sizeable mtDNA variability we scored, and the possible identification of a new early radiating lineage further stress the need for an extensive and large-scale characterization of donkey nuclear genome diversity to identify hotspots of variation and aid the conservation of local breeds worldwide.

More people in the world depend on water buffalo for their livelihoods than on any other domesticated animals, but its genetics is still not extensively explored. The 1000 Buffalo Genomes Project (1000BGP) provides genetic resources for global buffalo population study and tools to breed more sustainable and productive buffaloes. Here we report the most contiguous swamp buffalo genome assembly (PCC_UOA_SB_1v2) with substantial resolution of telomeric and centromeric repeats, ∼4-fold more contiguous than the existing reference river buffalo assembly and exceeding a recently published male swamp buffalo genome. This assembly was used along with the current reference to align 140 water buffalo short-read sequences and produce a public genetic resource with an average of ∼41 million single nucleotide polymorphisms per swamp and river buffalo genome. Comparison of the swamp and river buffalo sequences showed ∼1.5% genetic differences, and estimated divergence time occurred 3.1 million years ago (95% CI, 2.6-4.9). The open science model employed in the 1000BGP provides a key genomic resource and tools for a species with global economic relevance.

Sperm motility is directly related to the ability of sperm to move through the female reproductive tract to reach the ovum. Sperm motility is a complex trait that is influenced by environmental and genetic factors and is associated with male fertility, oocyte penetration rate, and reproductive success of cattle. In this study we carried out a GWAS in Italian Holstein bulls to identify candidate regions and genes associated with variations in progressive and total motility (PM and TM, respectively). After quality control, the final data set consisted of 5,960 records from 949 bulls having semen collected in 10 artificial insemination stations and genotyped at 412,737 SNPs (call rate >95%; minor allele frequency >5%). (Co)variance components were estimated using single trait mixed models, and associations between SNPs and phenotypes were assessed using a genomic BLUP approach. Ten windows that explained the greatest percentage of genetic variance were located on Bos taurus autosomes 1, 2, 4, 6, 7, 23, and 26 for TM and Bos taurus autosomes 1, 2, 4, 6, 8, 16, 23, and 26 for PM. A total of 150 genes for TM and 72 genes for PM were identified within these genomic regions. Gene Ontology enrichment analyses identified significant Gene Ontology terms involved with energy homeostasis, membrane functions, sperm-egg interactions, protection against oxidative stress, olfactory receptors, and immune system. There was significant enrichment of quantitative trait loci for fertility, calving ease, immune response, feed intake, and carcass weight within the candidate windows. These results contribute to understanding the architecture of the genetic control of sperm motility and may aid in the development of strategies to identify subfertile bulls and improve reproductive success.

The question of how local adaptation takes place remains a fundamental question in evolutionary biology. The variation of allele frequencies in genes under selection over environmental gradients remains mainly theoretical and its empirical assessment would help understanding how adaptation happens over environmental clines. To bring new insights to this issue we set up a broad framework which aimed to compare the adaptive trajectories over environmental clines in two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at putatively adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the 430 candidate adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different putative mechanisms involved in local adaptation in these two closely related species. Interestingly, the genomes of the 2 species were impacted differently by the environment, genes related to signatures of selection were most related to altitude, slope and rainfall seasonality for sheep, and summer temperature and spring rainfall for goats. The diversity of candidate adaptive pathways may result from a high number of biological functions involved in the adaptations to multiple eco-climatic gradients, and a differential role of climatic drivers on the two species, despite their co-distribution along the same environmental gradients. This study describes empirical examples of clinal variation in putatively adaptive alleles with different patterns in allele frequency distributions over continuous environmental gradients, thus showing the diversity of genetic responses in adaptive landscapes and opening new horizons for understanding genomics of adaptation in mammalian species and beyond.

In contrast to nuclear markers routinely used for genomic selection, mitogenome information has been underutilized for breeding and biodiversity management of cattle populations. Our main goal was to promote the efficient use of mitogenome SNPs contained in commercial high-throughput SNP arrays. In collaboration with NEOGEN Genomics (Lincoln, NE, USA), we integrated 310 SNPs into the commercial GGP Bovine 100K SNP array. In doing so, we demonstrated how mitogenome SNPs can be used in high-throughput arrays to (i) analyze population structure and diversity, (ii) classify bovine haplogroups and identify introgression and/or upgrading, (iii) screen and identify pedigree defects, (iv) impute mitogenome information on maternal lineages to increase statistical power in estimating the effects of mitogenome variation on quantitative production traits, and (v) identify deleterious mutations found in humans. In addition, we have developed protocols and pipelines inte-grated with the Magellan v2.0 software to enable efficient and routine use of mitogenome information in cattle breeding and genetic diversity management. Finally, we have highlighted some other interesting opportunities for the use of mitogenome information in the near future.

The Montecristo wild goat is an endangered feral population that has been on the homonymous island in the Tuscan Archipelago since ancient times. The origins of Montecristo goats are still debated, with authors dating their introduction either back to Neolithic times or between the 6th and 13th century of the Common Era. To investigate the evolutionary history and relationships of this population we assembled a 50K SNP dataset including 55 Mediterranean breeds and two nuclei of Montecristo goats sampled on the island and from an ex situ conservation project. Diversity levels, gene flow, population structure, and genetic relationships were assessed through multiple approaches. The insular population scored the lowest values of both observed and expected heterozygosity, highlighting reduced genetic variation, while the ex situ nucleus highlighted a less severe reduction. Multivariate statistics, network, and population structure analyses clearly separated the insular nucleus from all other breeds, including the population of Montecristo goats from the mainland. Moreover, admixture and gene flow analyses pinpointed possible genetic inputs received by the two Montecristo goat nuclei from different sources, while Runs of Homozygosity (ROHs) indicated an ancient bottleneck/founder effect in the insular population and recent extensive inbreeding in the ex situ one. Overall, our results suggest that Montecristo goats experienced several demographic fluctuations combined with admixture events over time and highlighted a noticeable differentiation between the two nuclei.

By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY and DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes, Y1A, Y1B, Y2A and Y2B, with a marked geographical partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and seven wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during migrations into northern Europe, eastern and southern Asia, and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographical range.