The aim of our research was the evaluation of the maternal genetic background of two Hungarian autochthonous sheep breeds of different geographical origin. A major argument for the preservation of endangered animal breeds is their documented past and historical importance. These also include the registration of pedigree data. This is the first study to evaluate and compare Tsigai and Cikta sheep in Hungary. Our investigation is based on two complete sequences of mitochondrial DNA (cytochrome b gene and control region). Our research was performed on these two sheep breeds with markedly different breed histories and breed characteristics to determine a possible common maternal genetic background, as ultimately the origin of both breeds can be traced back to Asia Minor. Between 2015 and 2017, a total of 203 biological samples were taken using a newly introduced founder sampling method. We found that the prevailing haplogroup B accounted for over 80% of both breeds, strengthening the common ancestral root. However, the pairwise genetic differentiation estimates (K_ST) calculated using the sequence-based statistics for cytochrome b gene and control region were 0.034 and 0.021, respectively (both at level p < 0.05); thus, revealing genetic differentiation in both sequences between the Tsigai and Cikta. We note that the known different history of the breeds is clearly justified by the currently studied deviations in their maternal genetic background.

The Szekler horse was a small-sized mountain horse of the Carpathian Mountains whose official stud book ceased to exist after WWII. Despite that, individual horses preserving all the characteristics of the Szekler horse remained scattered in remote areas. This study aims to evaluate the mitochondrial D-loop sequence (608 bp) of the founder population (n = 59) in 2021 of a breed reconstruction project started in 2012. D-loop showed 68 polymorphic sites. The number of haplotypes was 34, with haplotype diversity (Hd) 0.966 and nucleotide diversity (π) 0.02232. The value of Fu’s Fs statistic (−6.566) was significant (p < 0.001), which rejects a stable population status. Thirteen haplogroups (HG) were found with a nearly equal number of representatives (HG(n)—A (5), D (1), E (2), G (4), I (4), J–K (1), M (4), N (2), O’P (4), and R (1)). In contrast, the Q, L, and B HGs occurred in more horses (15, 9, and 7, respectively). Based on a large number of polymorphic sites and haplotypes, the founder stock is considered diverse. Since the HG Q is characteristic of Asian horses, the examined stock haplotype distribution reflects the eastern origin of the Hungarian horses brought from the East in 896 AD. It is complemented by the gene pool of horses from Europe (e.g., L) and the Middle East (e.g., B).

Knowing the sex of the animal that deposited a scat adds value to non-invasive monitoring, but read-ratio sexing methods were developed for human ancient DNA. We examined their use in shotgun metagenomes of seven stone marten (Martes foina) and red fox (Vulpes vulpes) scats. Human DNA, present in every library, was removed by competitive mapping against the host assembly and the human reference. Applying the Skoglund Ry metric to the marten samples yielded 0 to 25 Y-mapping reads per sample and failed to identify either of the two animals that Rx places firmly in the male range, so we adopted the X-to-autosome ratio Rx of Mittnik et al. instead, reimplemented as an open-source, species-agnostic Python tool. To test whether its human-derived thresholds transfer, we simulated female and male genomes of both species and drew 200 replicate subsamples at each of fourteen depths from 1,000 to 100,000 mapped reads. Nine of 11,200 replicates were assigned to the wrong sex, all of them below 2,000 mapped reads; above that depth the only failure was non-assignment, in under 5% of replicates above 7,500 reads and under 1% above 15,000. Applied to the scats, Rx identified four females and two males; one sample with 596 host-assigned reads was left unassigned. With competitive removal of human reads, Rx and its original thresholds are usable in these carnivores.

The Hungarian Grey (HG) cattle breed was almost extinct after WW2; only 200 cows and six bulls survived. Despite the historical significance of the HG, no comprehensive genomic analysis has been conducted to clarify its genetic diversity and evolutionary history. Previous studies have relied on random or limited pedigree sampling, lacking a fully representative dataset determining genetic and conservation status. Here, the founder sampling of 110 individuals and the analysis of their mitochondrial DNA (mtDNA) sequence variation aim to investigate the phylogenetic placement of the breed using, for the first time, a fully representative sample. All identified haplogroups belong to the taurine T macro-haplogroup, with a predominance of T3 (89.1%), followed by T2 (4.5%), T1 (3.6%), and T1′2′3 (2.7%). The phylogenetic analysis confirms the absence of ancient haplogroups derived from European aurochs, suggesting a purely taurine origin for the HG breed. The high haplotype diversity (Hd = 0.94) and the genetic similarity to other Podolian breeds, particularly Maremmana cattle, indicate a preserved genetic background despite centuries of selective breeding. The lack of intensive crossbreeding practices has maintained the original beef production purpose of the breed, distinguishing it from the crossbred Podolian cattle used for dual-purpose or dairy production.