Inferring fine-scale mutation and recombination rate maps in aye-ayes (Daubentonia madagascariensis) DOI Open Access
Vivak Soni, Cyril J. Versoza, John W. Terbot

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 28, 2024

The rate of input new genetic mutations, and the at which that variation is reshuffled, are key evolutionary processes shaping genomic diversity. Importantly, these rates vary not just across populations species, but also individual genomes. Despite previous studies having demonstrated failing to account for heterogeneity genome can bias inference both selective neutral population processes, mutation recombination maps have date only been generated a relatively small number organisms. Here, we infer such fine-scale aye-aye ( Daubentonia madagascariensis ) - highly endangered strepsirrhine represents one earliest splits in primate clade, thus stands as an important outgroup more commonly-studied haplorrhines utilizing recently released fully-annotated combined with high-quality sequencing data. We compare our indirectly inferred pedigree-based estimates, finding further evidence low aye-ayes compared other primates.

Язык: Английский

Estimating the distribution of fitness effects in aye-ayes (Daubentonia madagascariensis), accounting for population history as well as mutation and recombination rate heterogeneity DOI Open Access
Vivak Soni, Cyril J. Versoza, Susanne P. Pfeifer

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Янв. 3, 2025

ABSTRACT The distribution of fitness effects (DFE) characterizes the range selection coefficients from which new mutations are sampled, and thus holds a fundamentally important role in evolutionary genomics. To date, DFE inference primates has been largely restricted to haplorrhines, with limited data availability leaving other suborder primates, strepsirrhines, under-explored. advance our understanding population genetics this taxonomic group, we here map exonic divergence aye-ayes ( Daubentonia madagascariensis ) – only extant member Daubentoniidae family Strepsirrhini suborder. We further infer highly-endangered species, utilizing recently published high-quality annotated reference genome, well-supported model demographic history, as well both direct indirect estimates underlying mutation recombination rates. inferred is generally characterized by greater proportion deleterious relative humans, providing evidence larger long-term effective size. In addition however, immune-related sensory-related genes were found be amongst most rapidly evolving aye-aye genome.

Язык: Английский

Процитировано

1
Characterizing the Rates and Patterns of De Novo Germline Mutations in the Aye-Aye (Daubentonia madagascariensis) DOI Creative Commons
Cyril J. Versoza, Erin E. Ehmke, Jeffrey D. Jensen

и другие.

Molecular Biology and Evolution, Год журнала: 2025, Номер 42(3)

Опубликована: Март 1, 2025

Given the many levels of biological variation in mutation rates observed to date primates-spanning from species individuals genomic regions-future steps our understanding rate evolution will not only be aided by a greater breadth coverage across primate clade but also depth as afforded an evaluation multiple trios within individual species. In order help bridge these gaps, we here present analysis representing one most basal splits on tree (aye-ayes), combining whole-genome sequencing seven parent-offspring three-generation pedigree with novel computational pipeline that takes advantage recently developed pan-genome graphs, thereby circumventing application (highly subjective) quality metrics has previously been shown result notable differences detection de novo mutations and ultimately estimates rates. This deep sampling enabled both detailed picture parental age effects sex dependency rates, which compare studied primates, provided unique insights into nature genetic endangered primates planet.

Язык: Английский

Процитировано

1
A pedigree-based map of crossovers and non-crossovers in aye-ayes (Daubentonia madagascariensis) DOI Creative Commons
Cyril J. Versoza,

Audald Lloret-Villas,

Jeffrey D. Jensen

и другие.

Опубликована: Ноя. 11, 2024

Gaining a better understanding of rates and patterns meiotic recombination is crucial for improving evolutionary genomic modelling, with applications ranging from demographic to selective inference. Although previous research has provided important insights into the landscape crossovers in humans other haplorrhines, our both considerably more common outcome (i.e., non-crossovers) as well landscapes distantly-related primates strepsirrhines) remains limited owing difficulties associated identification non-crossover tracts species sampling. Thus, order elucidate this under-studied branch primate clade, we here characterize crossover aye-ayes utilizing whole-genome sequencing data six three-generation pedigrees three two-generation multi-sibling families, so doing provide novel process shaping diversity one world's most critically endangered species.

Язык: Английский

Процитировано

7
Characterizing the rates and patterns ofde novogermline mutations in the aye-aye (Daubentonia madagascariensis) DOI Creative Commons
Cyril J. Versoza, Erin E. Ehmke, Jeffrey D. Jensen

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Ноя. 11, 2024

Given the many levels of biological variation in mutation rates observed to date primates - spanning from species individuals genomic regions future steps our understanding rate evolution will be aided by both a greater breadth coverage across primate clade, but also depth as afforded an evaluation multiple trios within individual species. In order help bridge these gaps, we here present analysis representing one most basal splits on tree (aye-ayes), combining whole-genome sequencing seven parent-offspring three-generation pedigree with novel computational pipeline that takes advantage recently developed pan-genome graphs, thereby circumventing application (highly subjective) quality metrics has previously been shown result notable differences detection

Язык: Английский

Процитировано

7
Inferring the demographic history of aye-ayes (Daubentonia madagascariensis) from high-quality, whole-genome, population-level data DOI Creative Commons
John W. Terbot, Vivak Soni, Cyril J. Versoza

и другие.

Опубликована: Ноя. 11, 2024

The nocturnal aye-aye,

Язык: Английский

Процитировано

7
The landscape of structural variation in aye-ayes (Daubentonia madagascariensis) DOI Creative Commons
Cyril J. Versoza, Jeffrey D. Jensen, Susanne P. Pfeifer

и другие.

Опубликована: Ноя. 11, 2024

Aye-ayes (

Язык: Английский

Процитировано

7
Inferring demographic and selective histories from population genomic data using a two-step approach in species with coding-sparse genomes: an application to human data DOI Creative Commons
Vivak Soni, Jeffrey D. Jensen

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Сен. 22, 2024

The demographic history of a population, and the distribution fitness effects (DFE) newly arising mutations in functional genomic regions, are fundamental factors dictating both genetic variation evolutionary trajectories. Although DFE inference has been performed extensively humans, these approaches have generally either limited to simple models involving single or, where complex population inferred, without accounting for potentially confounding selection at linked sites. Taking advantage coding-sparse nature genome, we propose 2-step approach which coalescent simulations first used infer multi-population model, utilizing large non-functional regions that likely free from background selection. We then use forward-in-time perform conditional on demography inferred expected estimation procedure. Throughout, recombination mutation rate maps were account underlying empirical heterogeneity across human genome. Importantly, within this framework it is possible utilize fit multiple aspects data, scheme represents generalized such large-scale species with genomes.

Язык: Английский

Процитировано

6
Inferring fine-scale mutation and recombination rate maps in aye-ayes (Daubentonia madagascariensis) DOI Open Access
Vivak Soni, Cyril J. Versoza, John W. Terbot

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 28, 2024

The rate of input new genetic mutations, and the at which that variation is reshuffled, are key evolutionary processes shaping genomic diversity. Importantly, these rates vary not just across populations species, but also individual genomes. Despite previous studies having demonstrated failing to account for heterogeneity genome can bias inference both selective neutral population processes, mutation recombination maps have date only been generated a relatively small number organisms. Here, we infer such fine-scale aye-aye ( Daubentonia madagascariensis ) - highly endangered strepsirrhine represents one earliest splits in primate clade, thus stands as an important outgroup more commonly-studied haplorrhines utilizing recently released fully-annotated combined with high-quality sequencing data. We compare our indirectly inferred pedigree-based estimates, finding further evidence low aye-ayes compared other primates.

Язык: Английский

Процитировано

2