Predicting risk of Alzheimer’s disease using polygenic risk scores developed for Parkinson’s disease DOI Creative Commons
Britney E. Graham, Scott M. Williams, Jason H. Moore

et al.

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Aug. 21, 2023

Abstract Background and Objectives The two most common neurodegenerative diseases are Alzheimer’s disease (AD) Parkinson’s (PD), both related to age affect millions of people across the world, especially as life expectancy increases in certain countries. Here, we explore potential predictiveness genetic risk AD PD separately then extent underlying shared genetics PD. Methods population estimates for were derived using a previously developed specific polygenic score (psPRS) regression-based SNP filtering method. To test overlap between PD, ran regression psPRSs versus prevalences filtered unfiltered PRS vice versa. We assessed gene-gene interaction pathway involvement KnowledgeBase ( AlzKB ) STRINGdb, respectively. Results psPRS was moderately predictive, while not. After filtering, improved strongly explained variation. ability predict versa, is poor. However, AD, highly predictive. Discussion Our results suggest that there correlation allele frequency prevalence, well an generally. better predictor than AD. call further research into general disease, despite previous lack evidence.

Language: Английский

Genetic Coupling of Mate Recognition Systems in the Genomic Era DOI
Michael G. Ritchie, Roger K. Butlin

Cold Spring Harbor Perspectives in Biology, Journal Year: 2024, Volume and Issue: unknown, P. a041437 - a041437

Published: Feb. 5, 2024

Michael G. Ritchie1 and Roger K. Butlin2,3 1Centre for Biological Diversity, University of St. Andrews, College Gate, Andrews KY16 9AJ, United Kingdom 2Ecology Evolutionary Biology, School Biosciences, The Sheffield, Sheffield S10 2TN, 3Department Marine Sciences, Gothenburg, 405 30 Göteborg, Sweden Correspondence: mgr{at}st-andrews.ac.uk; r.k.butlin{at}sheffield.ac.uk

Language: Английский

Citations

6
The molecular basis of phenotypic evolution: beyond the usual suspects DOI
Rong‐Chien Lin,

Bianca T Ferreira,

Yao‐Wu Yuan

et al.

Trends in Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: May 1, 2024

Language: Английский

Citations

4
Fate of a supergene in the shift from diploidy to polyploidy DOI Creative Commons
Emiliano Mora‐Carrera, Narjes Yousefi, Giacomo Potente

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 22, 2025

ABSTRACT Despite the evolutionary importance of supergenes, their properties in polyploids remain unexplored. Polyploid genomes are expected to undergo chromosomal rearrangements and gene losses over time, potentially affecting supergene architecture. The iconic distyly ( S -locus), controlling a floral heteromorphism with two self-incompatible morphs, has been well-documented diploids, but remains unknown polyploids. Primula , classic model for since Darwin, is ancestrally diploid distylous, yet polyploid, homostylous species single, self-compatible morph evolved repeatedly. intraspecific loss associated small loss-of-function mutations -locus CYP T style length female self-incompatibility. Over longer timescales, relaxed selection on should generate greater accumulation larger mutations, including exon loss. By analyzing first assembled genome an allotetraploid, grandis ) comparative framework, we discovered two, nearly identical alleles same subgenome, suggesting it originated via inter-specific hybridization between distylous progenitor. Conformant predictions from theory, macroevolutionary coincided considerable degeneration while other genes remained largely unaffected, shift homostyly preceded facilitated polyploid establishment. At whole-genome level, found minimal subgenome dominance — as expected, given inferred recent origin P. highly reduced genetic diversity, congruently its narrow distribution self-compatibility. This study provides comparison across ploidy levels reproductive systems, contributing new knowledge previously fate supergenes SIGNIFICANCE advances evolution by elucidating how (clusters tightly linked genes) evolve different sets chromosomes systems. newly broad provide outcrossers self-fertilizers. We one pair rather than per revealing cross self-incompatibility was considerably degenerated, because rest unaffected.

Language: Английский

Citations

0
Short-term evolutionary implications of an introgressed size-determining supergene in a vulnerable population DOI Creative Commons
Pierre Lesturgie, John S. S. Denton, Lei Yang

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 27, 2025

The Thorny Skate (Amblyraja radiata) is a vulnerable species displaying discrete size-polymorphism in the northwest Atlantic Ocean (NWA). We conducted whole genome sequencing of samples collected across its range. Genetic diversity was similar at all sampled sites, but we discovered ~ 31 megabase bi-allelic supergene associated with size polymorphism, larger allele having introgressed last ~160,000 years B.P. While both Gulf Maine (GoM) and Canadian (CAN) populations exhibit detected significant deficit heterozygotes longer stretches homozygosity GoM population. This suggests inbreeding driven by assortative mating for not CAN. Coalescent-based demographic modelling reveals strong migration between regions maintaining genetic variability recombining genome, preventing speciation morphs. study highlights short-term context-dependent evolutionary consequences size-determining providing new insights management species. thorny skate ocean discreet polymorphism. Here, authors have sequenced 49 individuals, finding locus that size.

Language: Английский

Citations

0
Breeding Climate-Resilient Sunflowers in the Climate Change Era: Current Breeding Strategies and Prospects DOI
R. Manivannan,

R. Sasikala,

R. P. Ramteke

et al.

Published: Jan. 1, 2025

Language: Английский

Citations

0
Determining zygosity with multiplex Kompetitive Allele-Specific PCR (mxKASP) genotyping DOI Creative Commons
Manon C. de Visser, Willem R. M. Meilink, Anagnostis Theodoropoulos

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 25, 2024

Abstract We introduce multiplex Kompetitive Allele-Specific PCR (mxKASP): a modification of ‘classical’ KASP genotyping that allows zygosity to be determined in diploid organisms. Rather than targeting SNP associated with single marker, mxKASP targets two non-homologous markers. show proof concept by applying the balanced lethal system Triturus newts, which individuals are known possess either: (1) zero copies 1A version chromosome 1 and 1B version; (2) one copy 1B; or (3) 1B. is successful amplifying both marker reaction (if present), allowing inferred. independently confirm our results approach. argue can applied rapidly economically determine zygostity organisms, for large number samples at once.

Language: Английский

Citations

3
Stepwise recombination suppression around the mating-type locus in an ascomycete fungus with self-fertile spores DOI Creative Commons

Nina Vittorelli,

Ricardo C. Rodrı́guez de la Vega, Alodie Snirc

et al.

PLoS Genetics, Journal Year: 2023, Volume and Issue: 19(2), P. e1010347 - e1010347

Published: Feb. 10, 2023

Recombination is often suppressed at sex-determining loci in plants and animals, self-incompatibility or mating-type fungi. In fungal ascomycetes, recombination suppression around the locus associated with pseudo-homothallism, i . e production of self-fertile dikaryotic sexual spores carrying two opposite mating types. This has been well studied species complexes from different families Sordariales : Podospora anserina Neurospora tetrasperma However, it unclear whether this intriguing association holds other species. We show here that Schizothecium tetrasporum , a fungus third family order also produces mostly was due to high frequency second meiotic division segregation locus, indicating occurrence single systematic crossing-over event between centromere, as P The typical organization, plus MAT1-1-1 pseudogene MAT1-2 haplotype. High-quality genome assemblies types analyses revealed region 1.47 Mb locus. detected three evolutionary strata, stepwise extension suppression. strata displayed no rearrangement transposable element accumulation but gene losses disruptions were present, precisely margins. Our findings indicate convergent evolution across multiple ascomycete particular pattern had extended stepwise. pseudo-homothallism lineages presence disruption limits are consistent recently proposed mechanism sheltering deleterious alleles explain

Language: Английский

Citations

9
PAV-spotter: using signal cross-correlations to identify Presence/Absence Variation in target capture data DOI Creative Commons
Manon C. de Visser, Chris van der Ploeg, Milena Cvijanović

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 29, 2024

Abstract High throughput sequencing technologies have become essential in the fields of evolutionary biology and genomics. When dealing with non-model organisms or genomic gigantism, whole genomes is still relatively costly therefore reduced-genome representations are frequently obtained, for instance by ‘target capture’ approaches. While computational tools exist that can handle target capture data identify small-scale variants such as single nucleotide polymorphisms micro-indels, options to large scale structural limited. To meet this need, we introduce PAV-spotter: a tool presence/absence variation (PAV) data. PAV-spotter conducts signal cross-correlation calculation, which distribution read counts per between samples different priori defined classes – e.g. male versus female, diseased healthy compared. We apply test our methodology studying Triturus newts: salamanders gigantic currently lack an annotated reference genome. newts suffer from hereditary disease kills half their offspring during embryogenesis. compare two types embryos, characterized unique deletions, those embryos. Our findings show helps expose variants, even face medium low coverage levels, sample sizes, background noise due mis-mapped reads. be used study underlying supergene systems absence genome assemblies. The code, including further explanation on how use customize it, available through GitHub repository: https://github.com/Wielstra-Lab/PAVspotter .

Language: Английский

Citations

2
A supergene in seaweed flies modulates male traits and female perception DOI Creative Commons
Swantje Enge, Claire Mérot,

Raimondas Mozūraitis

et al.

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2023, Volume and Issue: 290(2008)

Published: Oct. 11, 2023

Supergenes, tightly linked sets of alleles, offer some the most spectacular examples polymorphism persisting under long-term balancing selection. However, we still do not understand their evolution and persistence, especially in face accumulation deleterious elements. Here, show that an overdominant supergene seaweed flies, Coelopa frigida, modulates male traits, potentially facilitating disassortative mating promoting intraspecific polymorphism. Across two continents, Cf-Inv(1) strongly affected composition cuticular hydrocarbons (CHCs) but only weakly CHC females. Using gas chromatography-electroantennographic detection, females can sense CHCs there may be differential perception between genotypes. Combining our phenotypic results with RNA-seq data, candidate genes for biosynthesis primarily expression males Conversely, odorant detection were differentially expressed both sexes showed high levels divergence haplotypes. We suggest reduced recombination haplotypes have led to rapid mate preferences as well increasing linkage loci. Together this probably helped maintain despite effects homozygotes.

Language: Английский

Citations

6
Ecology, the pace‐of‐life, epistatic selection and the maintenance of genetic variation in life‐history genes DOI Creative Commons
Göran Arnqvist,

Locke Rowe

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(17), P. 4713 - 4724

Published: June 29, 2023

Evolutionary genetics has long struggled with understanding how functional genes under selection remain polymorphic in natural populations. Taking as a starting point that is ultimately manifestation of ecological processes, we spotlight an underemphasized and potentially ubiquitous effect may have fundamental effects on the maintenance genetic variation. Negative frequency dependency well-established emergent property density dependence ecology, because relative profitability different modes exploiting or utilizing limiting resources tends to be inversely proportional their population. We suggest this often generate negative frequency-dependent (NFDS) major loci affect rate-dependent physiological such metabolic rate, are phenotypically manifested polymorphism pace-of-life syndromes. When locus NFDS shows stable intermediate polymorphism, should epistatic involving large numbers more minor life-history (LH) traits. alternative alleles at show sign epistasis locus, associative will promote polygenic variation LH genes. provide examples kind could involved empirical avenues better inform us importance reach process.

Language: Английский

Citations

4