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Reduced representation sequencing (RRS) has proven to be a cost-effective solution for sequencing subsets of the genome in non-model species for large-scale studies. However, the targeted nature of RRS approaches commonly introduces large amounts of missing data, leading to reduced statistical power and biased estimates in downstream analyses. Genotype imputation, the statistical inference of missing sites across the genome, is a powerful alternative to overcome the caveats associated with missing sites. Typically, genotype imputation requires the presence of a reference panel of haplotypes, however, this is not always feasible for non-model species. In this issue of Molecular Ecology Resources, Mora-Márquez et al. (2024) develop gtImputation, an unsupervised machine learning imputation tool with an interactive GUI, which leverages information from the underlying data structure itself, without the need for a reference panel. They showcase that their method performs equally well and even surpasses existing haplotype-clustering and unsupervised machine learning algorithms, particularly for sites with low minor allele frequency (MAF) and for data sets with strong underlying population structure. This innovative framework adds to the ongoing efforts to expand the applicability of imputation to non-model species, offering the opportunity to apply varied types of analyses requiring dense sets of markers, while also maintaining lower sequencing costs., (© 2025 John Wiley & Sons Ltd.)

The multi-millenia long history between dogs and humans has placed them at the forefront of archeological and genomic research. Despite ongoing efforts including the analysis of ancient dog and wolf genomes, many questions remain regarding their geographic and temporal origins, and the microevolutionary processes that led to the diversity of breeds today. Although ancient genomes provide valuable information, their use is hindered by low depth of coverage and post-mortem damage, which inhibits confident genotype calling. In the present study, we assess how genotype imputation of ancient dog and wolf genomes, utilising a large reference panel, can improve the resolution provided by ancient datasets. Imputation accuracy was evaluated by down-sampling high coverage dog and wolf genomes to 0.05-2x coverage and comparing concordance between imputed and high coverage genotypes. We measured the impact of imputation on principal component analyses and runs of homozygosity. Our findings show high (R 2 >0.9) imputation accuracy for dogs with coverage as low as 0.5x and for wolves as low as 1.0x. We then imputed a dataset of 90 ancient dog and wolf genomes, to assess changes in inbreeding during the last 10,000 years of dog evolution. Ancient dog and wolf populations generally exhibited lower inbreeding levels than present-day individuals. Interestingly, regions with low ROH density maintained across ancient and present-day samples were significantly associated with genes related to olfaction and immune response. Our study indicates that imputing ancient canine genomes is a viable strategy that allows for the use of analytical methods previously limited to high-quality genetic data.

Background: The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function., Results: We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection., Conclusions: We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

The evolutionary history of taxa with limited overseas dispersal abilities is considered to be majorly influenced by vicariant events constituting them as model organisms for the interpretation of evolutionary processes. An excellent candidate are the wall lizards of the genus Podarcis exhibiting an impressive level of genetic and morphological diversification and harboring several cases of recently discovered cryptic diversity. In this study, we investigated the effect of palaeogeographic events on the wall lizards' biodiversity patterns in the Aegean (Greece) as well as the evolutionary processes that acted both in space and time. To accomplish that we studied a group of three endemic Podarcis species (i.e., P. cretensis, P. levendis, and P. peloponnesiacus) both at the intra and interspecific levels employing mitochondrial and nuclear DNA sequence data as well as microsatellites. Furthermore, presence information coupled with bioclimatic data (i.e., species distribution modeling, and niche similarity analyses) shed light on the necessary ecological factors for the species' occurrence. These approaches revealed yet another case of cryptic diversity for this group of lizards, with the existence of two slightly overlapping lineages within P. peloponnesiacus and highly structured populations within P. cretensis. Species diversification occurred during the Pliocene with P. peloponnesiacus divergence into the two lineages dating back to 1.86 Mya. Furthermore, temperature and precipitation related environmental parameters were the most important ones regarding the current distribution of the studied species. Based on the results, we propose a more detailed phylogeographic scenario where both the paleogeography of the area and several environmental parameters have shaped the genetic diversity and the current distribution pattern of this species group., (Copyright © 2019 Elsevier Inc. All rights reserved.)