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Zoological Research Sep 2023The common marmoset ( ) has emerged as a valuable nonhuman primate model in biomedical research with the recent release of high-quality reference genome assemblies....
The common marmoset ( ) has emerged as a valuable nonhuman primate model in biomedical research with the recent release of high-quality reference genome assemblies. Epileptic marmosets have been independently reported in two Asian primate research centers. Nevertheless, the population genetics within these primate centers and the specific genetic variants associated with epilepsy in marmosets have not yet been elucidated. Here, we characterized the genetic relationships and risk variants for epilepsy in 41 samples from two epileptic marmoset pedigrees using whole-genome sequencing. We identified 14 558 184 single nucleotide polymorphisms (SNPs) from the 41 samples and found higher chimerism levels in blood samples than in fingernail samples. Genetic analysis showed fourth-degree of relatedness among marmosets at the primate centers. In addition, SNP and copy number variation (CNV) analyses suggested that the WW domain-containing oxidoreductase ( ) and Tyrosine-protein phosphatase nonreceptor type 21 ( ) genes may be associated with epilepsy in marmosets. Notably, gene deletion was more common in epileptic marmosets than control marmosets. This study provides valuable population genomic resources for marmosets in two Asian primate centers. Genetic analyses identified a reasonable breeding strategy for genetic diversity maintenance in the two centers, while the case-control study revealed potential risk genes/variants associated with epilepsy in marmosets.
Topics: Animals; Callithrix; Case-Control Studies; DNA Copy Number Variations; Genetics, Population; Epilepsy
PubMed: 37501399
DOI: 10.24272/j.issn.2095-8137.2022.514 -
Viruses Aug 2023Aspen mosaic-associated virus (AsMaV) is a newly identified , in the family , , associated with mosaic symptoms in aspen trees (). Aspen trees are widely distributed in...
Aspen mosaic-associated virus (AsMaV) is a newly identified , in the family , , associated with mosaic symptoms in aspen trees (). Aspen trees are widely distributed in Europe and understanding the population structure of AsMaV may aid in the development of better management strategies. The virus genome consists of five negative-sense single-stranded RNA (-ssRNA) molecules. To investigate the genetic diversity and population parameters of AsMaV, different regions of the genome were amplified and analyzed and full-length sequence of the divergent isolates were cloned and sequenced. The results show that RNA3 or nucleoprotein is a good representative for studying genetic diversity in AsMaV. Developed RT-PCR-RFLP was able to identify areas with a higher number of haplotypes and could be applied for screening the large number of samples. In general, AsMaV has a conserved genome and based on the phylogenetic studies, geographical structuring was observed in AsMaV isolates from Sweden and Finland, which could be attributed to founder effects. The genome of AsMaV is under purifying selection but not distributed uniformly on genomic RNAs. Distant AsMaV isolates displayed amino acid sequence variations compared to other isolates, and bioinformatic analysis predicted potential post-translational modification sites in some viral proteins.
Topics: Satellite Viruses; Finland; Sweden; Phylogeny; Genetics, Population; Mosaic Viruses
PubMed: 37632020
DOI: 10.3390/v15081678 -
Bio Systems Sep 2023In this work we present a systematic mathematical approximation scheme that exposes the way that information, about the evolutionary forces of selection and random...
In this work we present a systematic mathematical approximation scheme that exposes the way that information, about the evolutionary forces of selection and random genetic drift, is encoded within gene-frequency trajectories. We determine approximate, time-dependent, gene-frequency trajectory statistics, assuming additive selection. We use the probability of fixation to test and illustrate the approximation scheme introduced. For the case where the strength of selection and the effective population size have constant values, we show how a standard diffusion approximation result, for the probability of fixation, systematically emerges when increasing numbers of approximate trajectory statistics are taken into account. We then provide examples of how time-dependent parameters influence gene-frequency statistics.
Topics: Models, Genetic; Gene Frequency; Genetic Drift; Biological Evolution; Probability; Selection, Genetic; Genetics, Population
PubMed: 37488034
DOI: 10.1016/j.biosystems.2023.104982 -
Nature Reviews. Genetics Jan 2024In population genetics, the emergence of large-scale genomic data for various species and populations has provided new opportunities to understand the evolutionary... (Review)
Review
In population genetics, the emergence of large-scale genomic data for various species and populations has provided new opportunities to understand the evolutionary forces that drive genetic diversity using statistical inference. However, the era of population genomics presents new challenges in analysing the massive amounts of genomes and variants. Deep learning has demonstrated state-of-the-art performance for numerous applications involving large-scale data. Recently, deep learning approaches have gained popularity in population genetics; facilitated by the advent of massive genomic data sets, powerful computational hardware and complex deep learning architectures, they have been used to identify population structure, infer demographic history and investigate natural selection. Here, we introduce common deep learning architectures and provide comprehensive guidelines for implementing deep learning models for population genetic inference. We also discuss current challenges and future directions for applying deep learning in population genetics, focusing on efficiency, robustness and interpretability.
Topics: Deep Learning; Genomics; Genetics, Population; Genome; Biological Evolution
PubMed: 37666948
DOI: 10.1038/s41576-023-00636-3 -
Molecular Ecology Aug 2023Advancements in environmental DNA (eDNA) approaches have allowed for rapid and efficient species detections in diverse environments. Although most eDNA research is... (Review)
Review
Advancements in environmental DNA (eDNA) approaches have allowed for rapid and efficient species detections in diverse environments. Although most eDNA research is focused on leveraging genetic diversity to identify taxa, some recent studies have explored the potential for these approaches to detect within-species genetic variation, allowing for population genetic assessments and abundance estimates from environmental samples. However, we currently lack a framework outlining the key considerations specific to generating, analysing and applying eDNA data for these two purposes. Here, we discuss how various genetic markers differ with regard to genetic information and detectability in environmental samples and how analysis of eDNA samples differs from common tissue-based analyses. We then outline how it may be possible to obtain species absolute abundance estimates from eDNA by detecting intraspecific genetic variation in mixtures of DNA under multiple scenarios. We also identify the major causes contributing to allele detection and frequency errors in eDNA data, discuss their consequences for population-level analyses and outline bioinformatic approaches to detect and remove erroneous sequences. This review summarizes the key advances required to harness the full potential of eDNA-based intraspecific genetic variation to inform population-level questions in ecology, evolutionary biology and conservation management.
Topics: DNA, Environmental; Biodiversity; DNA Barcoding, Taxonomic; Environmental Monitoring; Genetics, Population; Genetic Variation
PubMed: 37254233
DOI: 10.1111/mec.17031 -
Global Change Biology Aug 2023As urbanization continues to increase, it is expected that two-thirds of the human population will reside in cities by 2050. Urbanization fragments and degrades natural...
As urbanization continues to increase, it is expected that two-thirds of the human population will reside in cities by 2050. Urbanization fragments and degrades natural landscapes, threatening wildlife including economically important species such as bees. In this study, we employ whole genome sequencing to characterize the population genetics, metagenome and microbiome, and environmental stressors of a common wild bee, Ceratina calcarata. Population genomic analyses revealed the presence of low genetic diversity and elevated levels of inbreeding. Through analyses of isolation by distance, resistance, and environment across urban landscapes, we found that green spaces including shrubs and scrub were the most optimal pathways for bee dispersal, and conservation efforts should focus on preserving these land traits to maintain high connectivity across sites for wild bees. Metagenomic analyses revealed landscape sites exhibiting urban heat island effects, such as high temperatures and development but low precipitation and green space, had the highest taxa alpha diversity across all domains even when isolating for potential pathogens. Notably, the integration of population and metagenomic data showed that reduced connectivity in urban areas is not only correlated with lower relatedness among individuals but is also associated with increased pathogen diversity, exposing vulnerable urban bees to more pathogens. Overall, our combined population and metagenomic approach found significant environmental variation in bee microbiomes and nutritional resources even in the absence of genetic differentiation, as well as enabled the potential early detection of stressors to bee health.
Topics: Animals; Bees; Humans; Urbanization; Cities; Metagenomics; Hot Temperature; Genetics, Population; Ecosystem
PubMed: 37173859
DOI: 10.1111/gcb.16757 -
Trends in Genetics : TIG Nov 2023Genetic biodiversity is rapidly gaining attention in global conservation policy. However, for almost all species, conservation relevant, population-level genetic data... (Review)
Review
Genetic biodiversity is rapidly gaining attention in global conservation policy. However, for almost all species, conservation relevant, population-level genetic data are lacking, limiting the extent to which genetic diversity can be used for conservation policy and decision-making. Macrogenetics is an emerging discipline that explores the patterns and processes underlying population genetic composition at broad taxonomic and spatial scales by aggregating and reanalyzing thousands of published genetic datasets. Here we argue that focusing macrogenetic tools on conservation needs, or conservation macrogenetics, will enhance decision-making for conservation practice and fill key data gaps for global policy. Conservation macrogenetics provides an empirical basis for better understanding the complexity and resilience of biological systems and, thus, how anthropogenic drivers and policy decisions affect biodiversity.
Topics: Conservation of Natural Resources; Biodiversity; Genetics, Population; Ecosystem
PubMed: 37648576
DOI: 10.1016/j.tig.2023.08.002 -
Current Opinion in Insect Science Oct 2023Monarch butterflies have emerged as a model system in migration genetics. Despite inherent challenges associated with studying the integrative phenotypes that... (Review)
Review
Monarch butterflies have emerged as a model system in migration genetics. Despite inherent challenges associated with studying the integrative phenotypes that characterize migration, recent research has highlighted genes and transcriptional networks underlying aspects of the monarch's migratory syndrome. Circadian clock genes and the vitamin A synthesis pathway regulate reproductive diapause initiation, while diapause termination appears to involve calcium and insulin signaling. Comparative approaches have highlighted genes that distinguish migratory and nonmigratory monarch populations, as well as genes associated with natural variation in propensity to initiate diapause. Population genetic techniques demonstrate that seasonal migration can collapse patterns of spatial structure at continental scales, whereas loss of migration can drive differentiation between even nearby populations. Finally, population genetics can be applied to reconstruct the monarch's evolutionary history and search for contemporary demographic changes, which can provide relevant context for understanding recently observed declines in overwintering North American monarch numbers.
Topics: Animals; Butterflies; Animal Migration; Genetics, Population; Genomics; Diapause
PubMed: 37385346
DOI: 10.1016/j.cois.2023.101079 -
Current Protocols Dec 2023Individuals of European descent have historically been the focus of genetic studies and possess relatively homogenous genomes. As a result, analytical methods have been...
Individuals of European descent have historically been the focus of genetic studies and possess relatively homogenous genomes. As a result, analytical methods have been developed and optimized with such genomes in mind. African-descent and Latino individuals generally possess genomes of greater architectural complexity due to mosaic genomic ancestry, which can extensively and intricately impact phenotypic expression. As such, genetic analyses of admixed individuals require that genetic admixture be quantified to accurately model the impact of genetic variation on phenotypic expression. In this overview, we explore how fundamental genetic concepts such as linkage disequilibrium and differential allele frequency interact with genetic admixture to uniquely influence phenotypes in admixed individuals. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.
Topics: Humans; Gene Frequency; Genetics, Population; Linkage Disequilibrium; Phenotype; Genome, Human
PubMed: 38146906
DOI: 10.1002/cpz1.953 -
Molecular Ecology Mar 2024
Topics: Animals; Ecology; Conservation of Natural Resources; Genetics, Population; Awards and Prizes
PubMed: 38339857
DOI: 10.1111/mec.17290