Tree sequences as a general-purpose tool for population genetic inference

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

Опубликована: Фев. 21, 2024

ABSTRACT As population genetics data increases in size new methods have been developed to store genetic information efficient ways, such as tree sequences. These structures are computationally and storage efficient, but not interchangeable with existing used for many inference methodologies the use of convolutional neural networks (CNNs) applied alignments. To better utilize these we propose implement a graph network (GCN) directly learn from sequence topology node data, allowing applications without an intermediate step converting sequences alignment format. We then compare our approach standard CNN approaches on set previously defined benchmarking tasks including recombination rate estimation, positive selection detection, introgression demographic model parameter inference. show that can be learned using GCN perform well common accuracies roughly matching or even exceeding CNN-based method. become more widely research foresee developments optimizations this work provide foundation moving forward.

Язык: Английский

Sweeps in space: leveraging geographic data to identify beneficial alleles inAnopheles gambiae

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

Опубликована: Фев. 9, 2025

Abstract As organisms adapt to environmental changes, natural selection modifies the frequency of non-neutral alleles. For beneficial mutations, outcome this process may be a selective sweep, in which an allele rapidly increases and perhaps reaches fixation within population. Selective sweeps have well-studied effects on patterns local genetic variation panmictic populations, but much less is known about dynamics continuous space. In particular, because limited movement across landscape leads unique population structure, spatial influence trajectory selected mutations. Here, we use forward-in-time, individual-based simulations space study impact mutations as they sweep through show that changes joint distribution geographic range occupied by focal demonstrate signal can used identify sweeps. We then leverage in-progress malaria vector Anopheles gambiae , species under strong pressure from control measures. By considering space, multiple previously undescribed variants with potential phenotypic consequences, including im-pacting IR-associated genes altering protein structure properties. Our results novel for detecting data implications genomic surveillance understanding variation.

Язык: Английский

Patterns of Gene Flow in Anopheles coluzzii Populations From Two African Oceanic Islands

Evolutionary Applications, Год журнала: 2024, Номер 17(11)

Опубликована: Ноя. 1, 2024

ABSTRACT The malaria vector Anopheles coluzzii is widespread across West Africa and the sole species on islands of São Tomé Príncipe. Our interest in population genetics this these part an assessment their suitability for a field trial involving release genetically engineered A. . construct includes two genes that encode anti‐Plasmodium peptides, along with Cas9‐based gene drive. We investigated flow among subpopulations each island to estimate dispersal rates between sites. Sampling covered known range both islands. Spatial autocorrelation suggests 7 km be likely extent species, whereas estimates based convolutional neural network were roughly 3 km. This difference highlights complexity dynamics value using multiple approaches. analysis also revealed weak heterogeneity populations within but did identify areas weakly resistant or permissive flow. Overall, exist as single Mendelian populations. expect low‐threshold drive has minimal fitness impact should, once introduced, spread relatively unimpeded island.

Язык: Английский