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This research aims to estimate heritability and repeatability based on the data on milk production traits (MY – milk yield; FY – milk fat yield; FC – milk fat content; PY – milk protein yield and PC – milk protein content) as well as pedigree and genomic information. A total of 6,041 animals were included in the research, while 2,565 of them had data for milk production traits. In order to form a genomic relationship matrix, 58K SNP data were used for a total of 1,491 cows. Several software tools were used in the preparation and analysis of data, which were provided by the Central Breeding Organization, Department of Animal Science, Faculty of Agriculture, University of Novi Sad. PreGSF90, in combination with RENUMF90, was used for quality control of genomic information. Genetic analysis was performed in WOMBAT software by the REML using standard repeatability univariate analysis (BLUPpe) and repeatability models for genomic prediction (GBLUPpe and ssGBLUPpe). In all three analyses, the highest heritability (0.410, 0.378 and 0.389, respectively) and repeatability (0.449, 0.429 and 0.440, respectively) were calculated for FC. Heritability estimates for all other traits were lower. Heritability ranged from 0.158 to 0.185 for MY, from 0.166 to 0.178 for FY, from 0.141 to 0.154 for PY and from 0.135 to 0.221 for PC. Heritability estimates indicate that it is possible to achieve genetic improvement but it is necessary to introduce the best model for prediction of breeding values of cow.

Balancing selection is the process of selection that preserves various alleles within a population. Studying the areas undergoing balancing selection is essential, because it preserves genetic diversity in a population. Finding genes that exhibit signs of balancing selection during the domestication of cattle is the goal of this study. To identify regions where polymorphism has persisted in the cattle population for millions of years, we examined the genome of cattle. In this study, we used bovine SNP 50 k data to conduct a detailed genome-wide assessment of selection signatures for balancing selection. We have included the genotyped data from 427 animals, including five taurines, two crossbreds, and eight Indian cattle breeds. For this study, we employed Tajima's D approach to identify signature regions undergoing balancing selection. Using the NCBI database, PANTHER 17.0, and CattleQTL database, the annotation was carried out after finding the relevant areas under balancing selection. The number of genomic regions undergoing balancing selection in Ayrshire, Brown-Swiss, Frieswal, Gir, Guernsey, Hariana, Holstein Friesian, Jersey, Kankrej, Nelore, Ongole, Red Sindhi, Sahiwal, Tharparkar, and Vrindavani was 11, 13, 13, 19, 18, 11, 17, 14, 14, 12, 10, 12, 13, 13, and 11, respectively. We have observed multiple immune system-related genes going through balancing selection, including KIT, NFATC2, GBP4, LRRC32, SYT7, RAG1, RAG2, LOC513659, and ZBTB17. In our study, we found that the majority of the immune-related genes and a few genes associated with growth, reproduction, production, and adaptation are undergoing balancing selection. [ABSTRACT FROM AUTHOR]

Most of what is known about extra‐pair paternity in hole‐nesting birds derives from studies using artificial nesting sites, such as nestboxes. However, it has rarely been investigated whether inference drawn from breeding events taking place in nestboxes matches what would be observed under natural conditions, that is, in natural cavities. We here report on a variation in promiscuity in blue tits and great tits nesting in natural cavities and nestboxes in an urban forest in Warsaw, Poland. Specifically, we tested whether local breeding density, local breeding synchrony, and extra‐pair paternity (inferred from SNP data generated with a high‐throughput genotyping by sequencing method) differed between birds nesting in natural cavities and nestboxes. In both blue tits and great tits, the frequency of extra‐pair paternity was similar between the two cavity types. In blue tits, we observed shorter nearest neighbor distance, higher neighbor density, and higher synchronous neighbor density (i.e., density of fertile females) in nestboxes relative to natural cavities. No such pattern was found in great tits. Moreover, we detected a positive relationship between the proportion of extra‐pair offspring in the nest and neighbor density around the nest in blue tits. Our results revealed that the provisioning of nestboxes did not change rates of extra‐pair paternity, suggesting that conclusions drawn from nestbox studies might adequately represent the natural variation in extra‐pair matings in some species or sites. However, the observed differences in spatiotemporal components of breeding dynamics highlight the fact that these parameters should be carefully considered when comparing mating behavior across studies and/or sites. [ABSTRACT FROM AUTHOR]

The systematics of the Old World Spiranthes sinensis (Pers.) Ames species complex (Orchidaceae) has been complicated by its wide distribution and morphological variations. Within the species complex, S. australis Lindl. has been generally accepted as the only Spiranthes Rich. species distributed on the Japanese mainland. The present study provides morphological, phylogenetic, and ecological evidence for the recognition of S. hachijoensis Suetsugu as a new species of the S. sinensis species complex on the Japanese mainland. Spiranthes hachijoensis is morphologically similar to S. hongkongensis S.Y. Hu & Barretto and S. nivea T.P. Lin & W.M. Lin, sharing a degenerated rostellum, pollinia without a viscidium, and distinctly trilobed stigma. However, the taxon can be morphologically distinguished from S. hongkongensis by its glabrous rachis, ovaries, and sepals, and from S. nivea by its papillate labellum disc, larger papillate basal labellum callosities, and glabrous rachis, ovaries, and sepals. The autogamy and flowering phenology (i.e., earlier flowering) of S. hachijoensis are most likely responsible for premating isolation from the sympatric S. australis. A MIG-seq-based high-throughput molecular analysis indicated that the genetic difference between S. hachijoensis and its putative sister species S. sinensis is comparable to, or even greater than, the genetic difference between pairs of other species within the S. sinensis species complex. Our multifaceted approach strongly supports the recognition of S. hachijoensis as a morphologically, phenologically, phylogenetically, and ecologically distinct species. [ABSTRACT FROM AUTHOR]

Due to their reduced morphology, non-photosynthetic plants have been one of the most challenging groups to delimit to species level. The mycoheterotrophic genus Monotropastrum, with the monotypic species M. humile, has been a particularly taxonomically challenging group, owing to its highly reduced vegetative and root morphology. Using integrative species delimitation, we have focused on Japanese Monotropastrum, with a special focus on an unknown taxon with rosy pink petals and sepals. We investigated its flowering phenology, morphology, molecular identity, and associated fungi. Detailed morphological investigation has indicated that it can be distinguished from M. humile by its rosy pink tepals and sepals that are generally more numerous, elliptic, and constantly appressed to the petals throughout its flowering period, and by its obscure root balls that are unified with the surrounding soil, with root tips that hardly protrude. Based on genome-wide single-nucleotide polymorphisms, molecular data has provided clear genetic differentiation between this unknown taxon and M. humile. Monotropastrum humile and this taxon are associated with different Russula lineages, even when they are sympatric. Based on this multifaceted evidence, we describe this unknown taxon as the new species M. kirishimense. Assortative mating resulting from phenological differences has likely contributed to the persistent sympatry between these two species, with distinct mycorrhizal specificity. [ABSTRACT FROM AUTHOR]

The study of population genetic structure and historical dynamics of species with disjunct distribution can reveal the mechanisms through with they were formed. Pinus densiflora is an essential tree species with ecological and economic value, and its natural distribution shows a disjunct pattern. Using transcriptome-level SNP data from 220 samples representing 32 naturally-distributed populations in East Asia, we investigated Pinus densiflora genetic diversity and structure, divergence time, and ancestral distribution. We identified five subpopulations which diverged approximately 2.02–1.49 million years ago, and found relatively low genetic differentiation among the three large subpopulations (SL, JH, and JK). Northeast China is the most likely origin, and its current distribution is the result of dispersal and vicariance events. It migrated southwest through the Liaodong Peninsula to the Shandong Peninsula and southeast through the Korean Peninsula to Japan. These results provide a basis for the conservation and management of P. densiflora in the future and the evolutionary study of species with similar life histories. [ABSTRACT FROM AUTHOR]

Lineage‐based species definitions applying coalescent approaches to species delimitation have become increasingly popular. Yet, the application of these methods and the recognition of lineage‐only definitions have recently been questioned. Species delimitation criteria that explicitly consider both lineages and evidence for ecological role shifts provide an opportunity to incorporate ecologically meaningful data from multiple sources in studies of species boundaries. Here, such criteria were applied to a problematic group of mycoheterotrophic orchids, the Corallorhiza striata complex, analysing genomic, morphological, phenological, reproductive‐mode, niche, and fungal host data. A recently developed method for generating genomic polymorphism data–ISSRseq–demonstrates evidence for four distinct lineages, including a previously unidentified lineage in the Coast Ranges and Cascades of California and Oregon, USA. There is divergence in morphology, phenology, reproductive mode, and fungal associates among the four lineages. Integrative analyses, conducted in population assignment and redundancy analysis frameworks, provide evidence of distinct genomic lineages and a similar pattern of divergence in the extended data, albeit with weaker signal. However, none of the extended data sets fully satisfy the condition of a significant role shift, which requires evidence of fixed differences. The four lineages identified in the current study are recognized at the level of variety, short of comprising different species. This study represents the most comprehensive application of lineage + role to date and illustrates the advantages of such an approach. [ABSTRACT FROM AUTHOR]

The study of population genetic structure and historical dynamics of species with disjunct distribution can reveal the mechanisms through with they were formed. Pinus densiflora is an essential tree species with ecological and economic value, and its natural distribution shows a disjunct pattern. Using transcriptome-level SNP data from 220 samples representing 32 naturally-distributed populations in East Asia, we investigated Pinus densiflora genetic diversity and structure, divergence time, and ancestral distribution. We identified five subpopulations which diverged approximately 2.02–1.49 million years ago, and found relatively low genetic differentiation among the three large subpopulations (SL, JH, and JK). Northeast China is the most likely origin, and its current distribution is the result of dispersal and vicariance events. It migrated southwest through the Liaodong Peninsula to the Shandong Peninsula and southeast through the Korean Peninsula to Japan. These results provide a basis for the conservation and management of P. densiflora in the future and the evolutionary study of species with similar life histories.

Feature selection and machine learning algorithms can be used to analyze Single Nucleotide Polymorphisms (SNPs) data and identify potential disease biomarkers. Reproducibility of identified biomarkers is critical for them to be useful for clinical research; however, genotyping platforms and selection criteria for individuals to be genotyped affect the reproducibility of identified biomarkers. To assess biomarkers reproducibility, we collected five SNPs datasets from the database of Genotypes and Phenotypes (dbGaP) and explored several data integration strategies. While combining datasets can lead to a reduction in classification accuracy, it has the potential to improve the reproducibility of potential biomarkers. We evaluated the agreement among different strategies in terms of the SNPs that were identified as potential Parkinson's disease (PD) biomarkers. Our findings indicate that, on average, 93% of the SNPs identified in a single dataset fail to be identified in other datasets. However, through dataset integration, this lack of replication is reduced to 62%. We discovered fifty SNPs that were identified at least twice, which could potentially serve as novel PD biomarkers. These SNPs are indirectly linked to PD in the literature but have not been directly associated with PD before. These findings open up new potential avenues of investigation., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The reviewer DZ declared a shared affiliation with the author YM to the handling editor at the time of review.