Using Computational Simulations to Model Deleterious Variation and Genetic Load in Natural Populations DOI
Christopher C. Kyriazis, Jacqueline A. Robinson, Kirk E. Lohmueller

et al.

The American Naturalist, Journal Year: 2023, Volume and Issue: 202(6), P. 737 - 752

Published: July 17, 2023

AbstractDeleterious genetic variation is abundant in wild populations, and understanding the ecological conservation implications of such an area active research. Genomic methods are increasingly used to quantify impacts deleterious natural populations; however, these approaches remain limited by inability accurately predict selective dominance effects mutations. Computational simulations offer a complementary tool that can help overcome limitations, although have yet be widely employed. In this perspective article, we aim encourage genomics researchers adopt greater use computational aid deepening our populations. We first provide overview components simulation variation, describing key parameters involved models. Next, discuss several for validating Finally, compare validate recently proposed mutation models, demonstrating models based on estimates selection from experimental systems biased toward highly describe new model supported multiple orthogonal lines evidence example scripts implementing (https://github.com/ckyriazis/simulations_review).

Language: Английский

The complete sequence and comparative analysis of ape sex chromosomes DOI Creative Commons
Kateryna D. Makova, Brandon D. Pickett, Robert S. Harris

et al.

Nature, Journal Year: 2024, Volume and Issue: 630(8016), P. 401 - 411

Published: May 29, 2024

Abstract Apes possess two sex chromosomes—the male-specific Y chromosome and the X chromosome, which is present in both males females. The crucial for male reproduction, with deletions being linked to infertility 1 . vital reproduction cognition 2 Variation mating patterns brain function among apes suggests corresponding differences their chromosomes. However, owing repetitive nature incomplete reference assemblies, ape chromosomes have been challenging study. Here, using methodology developed telomere-to-telomere (T2T) human genome, we produced gapless assemblies of five great (bonobo ( Pan paniscus ), chimpanzee troglodytes western lowland gorilla Gorilla Bornean orangutan Pongo pygmaeus ) Sumatran abelii )) a lesser (the siamang gibbon Symphalangus syndactylus )), untangled intricacies evolution. Compared chromosomes, vary greatly size low alignability high levels structural rearrangements—owing accumulation lineage-specific ampliconic regions, palindromes, transposable elements satellites. Many genes expand multi-copy families some evolve under purifying selection. Thus, exhibits dynamic evolution, whereas more stable. Mapping short-read sequencing data these revealed diversity selection on than 100 individual apes. These are expected inform evolution conservation genetics non-human apes, all endangered species.

Language: Английский

Citations

59
Patterns of recombination in snakes reveal a tug-of-war between PRDM9 and promoter-like features DOI
Carla Hoge, Marc de Manuel, Mohamed Mahgoub

et al.

Science, Journal Year: 2024, Volume and Issue: 383(6685)

Published: Feb. 22, 2024

In some mammals, notably humans, recombination occurs almost exclusively where the protein PRDM9 binds, whereas in vertebrates lacking an intact

Language: Английский

Citations

23
Worldwide Late Pleistocene and Early Holocene population declines in extant megafauna are associated with Homo sapiens expansion rather than climate change DOI Creative Commons
Juraj Bergman, Rasmus Østergaard Pedersen, Erick J. Lundgren

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 24, 2023

The worldwide extinction of megafauna during the Late Pleistocene and Early Holocene is evident from fossil record, with dominant theories suggesting a climate, human or combined impact cause. Consequently, two disparate scenarios are possible for surviving this time period - they could have declined due to similar pressures, increased in population size reductions competition other biotic pressures. We therefore infer histories 139 extant species using genomic data which reveal declines 91% throughout Quaternary period, larger experiencing strongest decreases. Declines become ubiquitous 32-76 kya across all landmasses, pattern better explained by Homo sapiens expansion than changes climate. estimate that, consequence, total abundance, biomass, energy turnover decreased 92-95% over past 50,000 years, implying major human-driven ecosystem restructuring at global scale.

Language: Английский

Citations

44
Experimental estimates of germline mutation rate in eukaryotes: a phylogenetic meta-analysis DOI Creative Commons
Yiguan Wang, Darren J. Obbard

Evolution Letters, Journal Year: 2023, Volume and Issue: 7(4), P. 216 - 226

Published: June 19, 2023

Mutation is the ultimate source of all genetic variation, and over last 10 years ready availability whole-genome sequencing has permitted direct estimation mutation rate for many non-model species across tree life. In this meta-analysis, we make a comprehensive search literature estimates in eukaryotes, identifying 140 accumulation (MA) parent-offspring (PO) studies covering 134 species. Based on these data, revisit differences single-nucleotide (SNM) between different phylogenetic lineages update known relationships generation time, genome size, nucleotide diversity-while accounting nonindependence. We do not find significant difference MA PO estimated rates, but confirm that mammal plant have higher rates than arthropods unicellular eukaryotes lowest rates. are with longer times larger sizes, even when relationships. Moreover, although diversity positively correlated rate, gradient relationship significantly less one (on logarithmic scale), consistent populations smaller effective size. For 29 which data available, indel short deletions generally more common insertions. Nevertheless, despite recent progress, no either SNM or available majority deeply branching eukaryotic lineages-or most animal phyla. Even among charismatic megafauna, experimental remain unknown amphibia scarce reptiles fish.

Language: Английский

Citations

37
The divergence of mutation rates and spectra across the Tree of Life DOI Creative Commons
Michael Lynch, Farhan Ali, Tongtong Lin

et al.

EMBO Reports, Journal Year: 2023, Volume and Issue: 24(10)

Published: Aug. 24, 2023

Abstract Owing to advances in genome sequencing, stability has become one of the most scrutinized cellular traits across Tree Life. Despite its centrality all things biological, mutation rate (per nucleotide site per generation) ranges over three orders magnitude among species and several‐fold within individual phylogenetic lineages. Within major organismal groups, rates scale negatively with effective population size a amount functional DNA genome. This relationship is parsimoniously explained by drift‐barrier hypothesis, which postulates that natural selection typically operates reduce until further improvement thwarted power random genetic drift. this constraint, molecular mechanisms underlying replication fidelity repair are free wander, provided performance entire system maintained at prevailing level. The evolutionary flexibility bears on resolution several prior conundrums population‐genetic analysis raises challenges for future applications these areas.

Language: Английский

Citations

36
Variation in mutation, recombination, and transposition rates inDrosophila melanogasterandDrosophila simulans DOI Creative Commons
Yiguan Wang,

Paul McNeil,

R. Abdulazeez

et al.

Genome Research, Journal Year: 2023, Volume and Issue: 33(4), P. 587 - 598

Published: April 1, 2023

The rates of mutation, recombination, and transposition are core parameters in models evolution. They impact genetic diversity, responses to ongoing selection, levels load. However, even for key evolutionary model species such as Drosophila melanogaster simulans, few estimates these available, we have little idea how vary between individuals, sexes, or populations. Knowledge this variation is fundamental parameterizing genome Here, provide direct their a West African European population D. simulans Across 89 flies, observe 58 single-nucleotide mutations, 286 crossovers, transposable element (TE) insertions. Compared the melanogaster, find has lower mutation rate (1.67 × 10-9 site-1 gen-1 vs. 4.86 gen-1) (8.99 10-5 copy-1 23.36 gen-1), but higher recombination (3.44 cM/Mb 2.06 cM/Mb). similar significantly lower, not different, rate. Overall, paternal-derived mutations more frequent than maternal ones both species. Our study quantifies among different populations our will benefit future studies genetics.

Language: Английский

Citations

26
Why do sex chromosomes progressively lose recombination? DOI
Paul Jay, Daniel L. Jeffries, Fanny E. Hartmann

et al.

Trends in Genetics, Journal Year: 2024, Volume and Issue: 40(7), P. 564 - 579

Published: April 27, 2024

Language: Английский

Citations

14
High prevalence of PRDM9-independent recombination hotspots in placental mammals DOI Creative Commons
Julien Joseph, Djivan Prentout, Alexandre Laverré

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(23)

Published: May 29, 2024

In many mammals, recombination events are concentrated in hotspots directed by a sequence-specific DNA-binding protein named PRDM9. Intriguingly, PRDM9 has been lost several times vertebrates, and notably among it pseudogenized the ancestor of canids. absence PRDM9, tend to occur promoter-like features such as CpG islands. It thus proposed that one role could be direct away from PRDM9-independent hotspots. However, ability assessed only handful species, clear picture how much occurs outside PRDM9-directed mammals is still lacking. this study, we derived an estimator past activity based on signatures GC-biased gene conversion substitution patterns. We quantified 52 species boreoeutherian mammals. observe wide range rates at these loci: (such mice, humans, some felids, or cetaceans) show deficit recombination, while majority display peak recombination. Our results demonstrate can coexist their coexistence appears rule rather than exception. Additionally, location relatively more stable hotspots, but nevertheless evolve slowly concert with DNA hypomethylation.

Language: Английский

Citations

12
Meta-analysis shows no consistent evidence for senescence in ejaculate traits across animals DOI Creative Commons
Krish Sanghvi, Regina Vega‐Trejo, Shinichi Nakagawa

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Jan. 16, 2024

Abstract Male reproductive traits such as ejaculate size and quality, are expected to decline with advancing age due senescence. It is however unclear whether this expectation upheld across taxa. We perform a meta-analysis on 379 studies, quantify the effects of male 157 species non-human animals. Contrary predictions, we find no consistent pattern age-dependent changes in traits. This result partly reflects methodological limitations, studies sampling low proportion adult lifespan, or inability meta-analytical approaches document non-linear ageing trajectories traits; which could potentially lead an underestimation Yet, taxon-specific differences patterns For instance, older males produce less motile slower sperm ray-finned fishes, but larger ejaculates insects, compared younger males. Notably, lab rodents show senescence most measured. Our study challenges notion universal senescence, highlighting need for controlled methodologies more nuanced understanding cognisant biology, experimental design, selection pressures, life-history.

Language: Английский

Citations

10
Low-frequency somatic mutations are heritable in tropical trees Dicorynia guianensis and Sextonia rubra DOI
Sylvain Schmitt, Patrick Heuret, Valérie Troispoux

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(10)

Published: Feb. 27, 2024

Somatic mutations potentially play a role in plant evolution, but common expectations pertaining to somatic remain insufficiently tested. Unlike most animals, the germline is assumed be set aside late development, leading expectation that plants accumulate along growth. Therefore, several predictions were made on fate of mutations: have generally low frequency tissues; at high higher chance intergenerational transmission; branching topology tree dictates mutation distribution; and exposure UV (ultraviolet) radiation increases mutagenesis. To provide insights into accumulation transmission plants, we produced two high-quality reference genomes unique dataset 60 high-coverage whole-genome sequences tropical species, Dicorynia guianensis (Fabaceae) Sextonia rubra (Lauraceae). We identified 15,066 de novo D. 3,208 S. , surprisingly almost all found frequency. demonstrate 1) low-frequency can transmitted next generation; 2) phylogenies deviate from tree; 3) rates spectra are not demonstrably affected by differences exposure. Altogether, our results suggest far more complex links between growth, aging, exposure, than commonly thought.

Language: Английский

Citations

10