bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: Sept. 5, 2024
Most of our understanding the fundamental processes mutation and recombination stems from a handful disparate model organisms pedigree studies mammals, with little known about other vertebrates. To gain broader comparative perspective, we focused on zebra finch (
Language: Английский
eLife, Journal Year: 2023, Volume and Issue: 12
Published: June 6, 2023
The rates of appearance new mutations play a central role in evolution. However, mutational processes natural environments and their relationship with growth are largely unknown, particular tropical ecosystems high biodiversity. Here, we examined the somatic mutation landscapes two trees, Shorea laevis (slow-growing) S. leprosula (fast-growing), Borneo, Indonesia. Using newly constructed genomes, identified greater number trees than temperate trees. In both species, observed linear increase physical distance between branches. found that rate accumulation per meter was 3.7-fold higher . This difference scaled slower compared to leprosula, resulting constant year species. We also neutral within an individual, but those transmitted next generation subject purifying selection. These findings suggest accumulate absolute time older have contribution towards generating genetic variation.
Language: Английский
Citations
9
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown
Published: July 11, 2023
In vertebrates, there are two known mechanisms by which meiotic recombination is directed to the genome: in humans, mice, and other mammals, occurs almost exclusively where protein PRDM9 binds, while species lacking an intact
Language: Английский
Citations
9
Current Biology, Journal Year: 2023, Volume and Issue: 33(22), P. R1166 - R1172
Published: Nov. 1, 2023
Language: Английский
Citations
9
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: April 10, 2024
Estimates of de novo mutation rates are essential for phylogenetic and demographic analyses, but their inference has previously been impeded by high error in sequence data uncertainty the fossil record. Here, we directly estimate germline all extant members Panthera, as well closely related outgroup Neofelis nebulosa, using pedigrees. We use a validated pipeline (RatesTools) to calculate rate each species subsequently explore impacts novel on historic effective population size estimates these charismatic felids conservation concern. Importantly, find that choice reference genome, type coverage, individual impact rate. Despite stochastic effects, inferred base pair fell between 0.5 1.4e-08 per generation (mean 0.81e-08 +/- 0.35-08 across Pantherinae). Our results provide cautionary view inter-species comparisons, given associated with genome sequencing depth coverage individuals.
Language: Английский
Citations
3
eLife, Journal Year: 2024, Volume and Issue: 12
Published: Oct. 23, 2024
The rates of appearance new mutations play a central role in evolution. However, mutational processes natural environments and their relationship with growth are largely unknown, particular tropical ecosystems high biodiversity. Here, we examined the somatic mutation landscapes two trees, Shorea laevis (slow-growing) S. leprosula (fast-growing), Borneo, Indonesia. Using newly constructed genomes, identified greater number trees than temperate trees. In both species, observed linear increase physical distance between branches. found that rate accumulation per meter was 3.7-fold higher . This difference scaled slower compared to leprosula, resulting constant year species. We also neutral within an individual, but those transmitted next generation subject purifying selection. These findings suggest accumulate absolute time older have contribution towards generating genetic variation.
Language: Английский
Citations
3
Molecular Biology and Evolution, Journal Year: 2025, Volume and Issue: 42(4)
Published: March 25, 2025
Abstract Rates of molecular evolution are known to vary across species, often deviating from the classical expectation a strict clock. In many cases, rate has been found correlate generation time, an effect that could be explained if species with shorter times have higher mutation rates per year. We investigate this hypothesis using direct estimates for 133 eukaryotic diverse taxonomic groups. Using phylogenetic comparative approach, we find strong negative correlation between year and consistent all Our results provide simple explanation why time plays pivotal role in driving eukaryotes.
Language: Английский
Citations
0
PLoS Genetics, Journal Year: 2025, Volume and Issue: 21(4), P. e1011661 - e1011661
Published: April 15, 2025
Most of our understanding the fundamental processes mutation and recombination stems from a handful disparate model organisms pedigree studies mammals, with little known about other vertebrates. To gain broader comparative perspective, we focused on zebra finch ( Taeniopygia castanotis ), which, like birds, differs mammals in its karyotype (which includes many micro-chromosomes), mechanism by which is directed to genome, aspects ontogenesis. We collected genome sequences three generation pedigrees that provide information 80 meioses, inferring 202 single-point de novo mutations, 1,088 crossovers, 275 non-crossovers. On basis, estimated sex-averaged rate 5.0 × 10 -9 per base pair generation, par have similar time (~2–3 years). Also as found paternal germline bias at later stages gametogenesis (of 1.7:1) but no discernible difference between sexes early development. Examining patterns, crossover macro-chromosomes 0.93 cM/Mb, pronounced enrichment crossovers near telomeres. In contrast, non-crossover rates are more uniformly distributed. micro-chromosomes, substantially higher (3.96 cM/Mb), accordance homeostasis, both events At finer scale, overlap CpG islands often than expected chance, absence PRDM9. Estimates degree GC-biased gene conversion (59%), mean tract length (~32 bp), non-crossover-to-crossover ratio (5.4:1) all comparable those reported primates mice. Therefore, properties resolutions remain over large phylogenetic distances.
Language: Английский
Citations
0
Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(2)
Published: Feb. 1, 2024
Abstract Delayed fatherhood results in a higher risk of inheriting new germline mutation that might result congenital disorder the offspring. In particular, some FGFR3 mutations increase frequency with age, but there are still large number uncharacterized could be expanding male potentially early- or late-onset effects Here, we used digital polymerase chain reaction to assess and spatial distribution 10 different missense substitutions sexually mature germline. Our functional assessment receptor signaling variants biophysical methods showed 9 these resulted activation receptor´s downstream signaling, resulting 2 expansion behaviors. Variants form larger subclonal expansions dissected postmortem testis also positive correlation substitution sperm donor's high ligand-independent activation. contrast, measured elevated frequencies independent age did not measurable testis. This suggests promiscuous signal an accumulation before sexual maturation gonad clones staying relatively constant size throughout time. Collectively, provide novel insights into our understanding mutagenesis driver their mosaicism important consequences for transmission recurrence associated disorders.
Language: Английский
Citations
3
Genome Biology and Evolution, Journal Year: 2022, Volume and Issue: 14(10)
Published: Sept. 29, 2022
Abstract A male mutation bias is observed across vertebrates, and, where data are available, this accompanied by increased per-generation rates with parental age. While continuing mitotic cell division in the germline post puberty has been proposed as major cellular mechanism underlying both patterns, little direct evidence for role found. Understanding evolution of rate among species requires that we identify molecular mechanisms change between species. Here, study an extended pedigree brown (grizzly) bear, Ursus arctos horribilis. Brown bears hibernate one-third year, a period during which spermatogenesis slows or stops altogether. The reduction predicted to lessen and lower However, using whole-genome sequencing, find highly similar expected non-hibernating We also carry out phylogenetic comparison substitution along lineage leading bear panda (a species) no slowing hibernator. Our results contribute accumulating suggests not determinant biases. provide quantitative basis improved estimates timing carnivore evolution.
Language: Английский
Citations
12
Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(21), P. 5524 - 5537
Published: Aug. 25, 2022
The guppy Y chromosome has been considered a model system for the evolution of suppressed recombination between sex chromosomes, and it proposed that complete sex-linkage evolved across about 3 Mb surrounding this fish's sex-determining locus, followed by suppression further 7 23 XY pair, forming younger "evolutionary strata". Sequences genome show is very similar to X chromosome. Knowing which parts are completely nonrecombining, whether there indeed large nonrecombining region, important understanding its evolution. Here, we describe analyses PoolSeq data in samples from within multiple natural populations Trinidad, yielding new results support previous evidence occasional X. We detected recent demographic changes, notably downstream have higher synonymous site diversity than upstream ones other expected signals bottlenecks. associations sequence variants rather divergence under lack recombination. Although infrequent, frequent enough with SNPs can suggest region locus must be located. Diversity elevated physically chromosome, conforming predictions infrequent carries one or more sexually antagonistic polymorphisms. However, no consistently male-specific were found, supporting suggestion any sex-linked may small.
Language: Английский
Citations
11