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Genetics

The study of heredity and genetic variation, including molecular genetics, population genetics, genomics, epigenetics, genetic engineering, and the genetic basis of traits, evolution, and disease

22 papers

Papers

Paternal SARS-CoV-2 infection impacts sperm small noncoding RNAs and increases anxiety in offspring in a sex-dependent manner

This mouse study suggests that male SARS-CoV-2 infection can lead to increased anxiety-like behaviors in first-generation offspring and subtle changes in grand-offspring, mediated by alterations in sperm small noncoding RNAs. Microinjecting these altered sperm RNAs into oocytes partially replicated the anxiety phenotype. However, these findings are from an animal model and their direct relevance to humans requires further research.

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Genetics Oct 22, 06:48 PM

Challenges in structural variant calling in low-complexity regions

This paper highlights that structural variants (SVs) are notoriously difficult to detect accurately in low-complexity regions (LCRs) of the human genome, even with advanced long-read sequencing. While LCRs make up a small fraction of the genome, they harbor a disproportionately high percentage of confident SVs and are where the vast majority of SV calling errors occur. The study, based on a single human sample, underscores the critical need for specialized algorithms and careful analysis in these problematic genomic areas.

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Genetics Sep 30, 05:36 AM

1206 genomes reveal origin and movement of Aedes aegypti driving increased dengue risk

This study analyzed 1206 genomes of Aedes aegypti mosquitoes, revealing that the invasive subspecies (Aaa) likely emerged in the Americas after the Atlantic slave trade and spread globally. The research also highlights contemporary admixture between Aaa and the ancestral African subspecies (Aaf), including the sharing of insecticide-resistance mutations, posing a threat to dengue control efforts in Africa.

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Genetics Sep 22, 08:46 PM

Resolving out of Africa event for Papua New Guinean population using neural network

This study uses genomic data and simulations to challenge the previous idea that the Papua New Guinean population's unique genetic makeup comes from an extremely early migration out of Africa. Instead, they find a strong population bottleneck and slower growth are the primary reasons for the observed differences, suggesting PNG people are closely related to East Asians.

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Genetics Sep 19, 02:49 AM

Assessing temporal and geographic contacts across the Adriatic Sea through the analysis of genome-wide data from Southern Italy

This study analyzes genome-wide data from over 700 individuals around the South Mediterranean, including 102 from Southern Italy, combined with ancient DNA. The findings show close genetic ties between Southern Italians and Eastern Peloponnesians, suggesting interactions predating recent migrations. Some Southern Italians also exhibit a unique genetic component potentially linked to Bronze Age migrations from the Caucasus.

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Genetics Sep 06, 06:45 PM

Ancestry-inclusive dog genomics challenges popular breed stereotypes

This study, using owner surveys and genetic data from over 18,000 dogs, found that breed plays a surprisingly small role in predicting individual dog behavior, explaining only 9% of variation. While some breed tendencies exist, most behaviors are influenced by many genes and environmental factors, suggesting that breed stereotypes are often inaccurate. The study highlights the heritability of various behavioral traits, emphasizing the importance of both genetics and environment in shaping dog behavior.

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Genetics Aug 26, 04:48 PM

Tracing the stepwise Darwinian evolution of a plant halogenase

This study uses the genome of *Menispermum canadense* to trace the evolution of dechloroacutumine halogenase (DAH), a rare plant enzyme that adds chlorine to a compound. DAH likely evolved from a flavonol synthase gene through duplication, neofunctionalization, and gene loss events, requiring intermediate enzyme forms and specific mutations. The researchers use structural modeling and experiments to support this evolutionary trajectory.

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Genetics Aug 20, 08:53 AM

Unveiling the complexity of post-Roman polity formation using ancient DNA

Analysis of ancient DNA from seven sites in the Little Hungarian Plain shows a substantial increase of contemporary Northern European ancestry around 500 CE, coincident with the emergence of new communities and potentially associated with Langobard expansion. While regional genomic ancestry was similar, burial practices and biological relatedness patterns varied between communities, suggesting diverse local social organizations within this emerging polity.

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Genetics Aug 19, 05:07 PM

Unlocking the full potential of Oxford Nanopore reads with NOVOLoci

NOVOLoci is a new algorithm for assembling DNA sequences that can accurately reconstruct complex genomic regions, even with limited data. It performs particularly well in challenging regions linked to genetic disorders and enables the creation of phased diploid genomes from organisms where DNA is scarce. While slower than other assemblers, its increased accuracy makes it a powerful tool when phasing matters.

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Genetics Aug 17, 07:58 PM

Complete sequencing of ape genomes

This study presents complete, phased diploid genomes of six ape species, revealing greater divergence from humans than previously estimated, particularly in highly repetitive regions. The researchers also characterized the complete sequence and organization of acrocentric chromosomes, centromeres, subterminal heterochromatin, and lineage-specific segmental duplications, uncovering hundreds of new candidate genes and genomic features unique to ape lineages. Bonobos were found to have a bimodal distribution of centromere lengths, a previously unknown feature in primates.

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Genetics Aug 14, 08:18 AM

Ancient genomics support deep divergence between Eastern and Western Mediterranean Indo-European languages

This study used ancient DNA from 314 individuals, along with existing data, to investigate the spread of Indo-European languages around the Mediterranean. They found distinct genetic patterns in the west and east, suggesting different migration routes for language families like Italo-Celtic and Graeco-Armenian. This suggests that the ancestors of Greek and Armenian speakers arrived directly from Yamnaya groups to the east, while those in Western Europe had Bell Beaker ancestry.

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Genetics Aug 10, 07:37 PM

Dismantling a dogma: the inflated significance of neutral genetic diversity in conservation genetics

The paper argues that neutral genetic diversity is an insufficient indicator for conservation efforts and proposes that focusing on functional genetic diversity, demographic history, and ecological relationships is more crucial. It suggests that the relationship between neutral diversity, functional diversity, and fitness is complex and often unintuitive, advocating for precise mapping of adaptive genetic variation and better understanding of mutation load.

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Genetics Jul 14, 05:22 PM

A saturated map of common genetic variants associated with human height

Using a genome-wide association study of 5.4 million individuals, researchers identified 12,111 independent SNPs associated with height, accounting for almost all common SNP-based heritability. These SNPs cluster within specific genomic regions covering ~21% of the genome, with higher density regions enriched for genes related to skeletal growth. Prediction accuracy is high in European populations but lower in other ancestries, suggesting the need for greater diversity in future studies.

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Genetics Jul 14, 05:19 PM

Exome sequencing and analysis of 454,787 UK Biobank participants

This study analyzed exome sequencing data from 454,787 UK Biobank participants, identifying over 12 million coding variants and finding 564 genes associated with nearly 500 health-related traits. Most of these associations were independent of common variant signals found in genome-wide association studies, highlighting the potential of exome sequencing to pinpoint rare variants that influence disease risk and other traits.

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Genetics Jul 14, 05:07 PM

GAPIT Version 3: Boosting Power and Accuracy for Genomic Association and Prediction

GAPIT 3 enhances genomic analysis by implementing multiple loci tests (MLMM, FarmCPU, BLINK) for GWAS, improving power and speed. It also introduces compressed BLUP and SUPER BLUP for genomic prediction, catering to different trait architectures and heritability levels. Interactive visualizations and detailed reports further aid in data interpretation and method selection.

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Genetics Jul 14, 10:31 AM