Continent-wide genomic signatures of adaptation to urbanisation in a songbird across Europe

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: May 20, 2021

Urbanisation is increasing worldwide, and there now ample evidence of phenotypic changes in wild organisms response to this novel environment. Yet, the genetic genomic architecture underlying these adaptations are poorly understood. Here, we genotype 192 great tits (Parus major) from nine European cities, each paired with an adjacent rural site, address major knowledge gap our understanding wildlife urban adaptation. We find that a combination polygenic allele frequency shifts recurrent selective sweeps associated adaptation environments. While haplotypes under selection rarely shared across populations, occur within same genes, mostly linked neural function development. Collectively, show widespread songbird occurs through unique core-set behaviour-linked genes.

Language: Английский

---

Genome-wide parallelism underlies contemporary adaptation in urban lizards

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(3)

Published: Jan. 12, 2023

Urbanization drastically transforms landscapes, resulting in fragmentation, degradation, and the loss of local biodiversity. Yet, urban environments also offer opportunities to observe rapid evolutionary change wild populations that survive even thrive these novel habitats. In many ways, cities represent replicated “natural experiments” which geographically separated adaptively respond similar selection pressures over timescales. Little is known, however, about genetic basis adaptive phenotypic differentiation nor extent parallelism reflected at genomic level with signatures parallel selection. Here, we analyzed underpinnings urban-associated Anolis cristatellus , a small-bodied neotropical lizard found abundantly both urbanized forested environments. We show response environmental underlain by identify candidate loci across genome associated this morphological divergence. Our findings point polygenic on standing variation as key process effectuate adaptation. Identified several functions skeletomuscular development, morphology, human disease. Taken together, results shed light complex adaptations, provide insight into role contingency determinism adaptation environments, underscore value address fundamental questions.

Language: Английский

---

Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data

PLoS Genetics, Journal Year: 2021, Volume and Issue: 17(2), P. e1009373 - e1009373

Published: Feb. 26, 2021

Whether hard sweeps or soft dominate adaptation has been a matter of much debate. Recently, we developed haplotype homozygosity statistics that (i) can detect both and with similar power (ii) classify the detected as soft. The application our method to population genomic data from natural Drosophila melanogaster (DGRP) allowed us rediscover three known cases at loci Ace, Cyp6g1, CHKov1 be driven by sweeps, additional candidate for recent strong sweeps. Surprisingly, all top 50 candidates showed patterns more consistent rather than Harris et al. 2018 criticized this work, suggesting statistics, including positive controls, are unlikely instead these easily explained complex neutral demographic models. They also claim non-sweeps likely Here, reanalyze DGRP using range admixture models reconfirm original published results majority in D. first true second, they do appear Furthermore, discuss ways take work forward given most employed such analyses necessarily too simple capture full complexity, while realistic inferred correctly because require large number free parameters.

Language: Английский

---

Genomic consequences of domestication of the Siamese fighting fish

Science Advances, Journal Year: 2022, Volume and Issue: 8(10)

Published: March 9, 2022

Siamese fighting (betta) fish are among the most popular and morphologically diverse pet fish, but genetic bases of their domestication phenotypic diversification largely unknown. We assembled de novo genome a wild Betta splendens whole-genome sequenced 98 individuals across five closely related species. find evidence bidirectional hybridization between domesticated ornamental betta other discover dmrt1 as main sex determination gene in that it has lower penetrance B. . Furthermore, we genes with signatures recent, strong selection have large effects on color specific parts body or shape individual fins unlinked. Our results demonstrate how simple architectures paired anatomical modularity can lead to vast diversity generated during animal launch powerful new system for evolutionary genetics.

Language: Английский

---

A spatially aware likelihood test to detect sweeps from haplotype distributions

PLoS Genetics, Journal Year: 2022, Volume and Issue: 18(4), P. e1010134 - e1010134

Published: April 11, 2022

The inference of positive selection in genomes is a problem great interest evolutionary genomics. By identifying putative regions the genome that contain adaptive mutations, we are able to learn about biology organisms and their history. Here introduce composite likelihood method identifies recently completed or ongoing by searching for extreme distortions spatial distribution haplotype frequency spectrum along relative genome-wide expectation taken as neutrality. Furthermore, simultaneously infers two parameters sweep: number sweeping haplotypes "width" sweep, which related strength timing selection. We demonstrate this outperforms leading haplotype-based statistics, though strong signals low-recombination merit extra scrutiny. As control, apply it well-studied human populations from 1000 Genomes Project examine patterns at LCT MHC loci. also data set brown rats sampled NYC identify genes olfactory perception. To facilitate use method, have implemented user-friendly open source software.

Language: Английский

---

Adaptation to urban environments

Current Opinion in Insect Science, Journal Year: 2022, Volume and Issue: 51, P. 100893 - 100893

Published: Feb. 28, 2022

Language: Английский

---

The evolutionary history of wild and domestic brown rats ( Rattus norvegicus )

Science, Journal Year: 2024, Volume and Issue: 385(6715), P. 1292 - 1297

Published: Sept. 19, 2024

The brown rat ( Rattus norvegicus ) occupies nearly every terrestrial habitat with a human presence and is one of our most important model organisms. Despite this prevalence, gaps remain in understanding the evolution commensalism, their global dispersal, mechanisms underlying contemporary adaptations to diverse environments. In Review, we explore recent advances evolutionary history rats discuss key challenges, including finding accurately dating historical specimens, disentangling histories multiple domestication events, synthesizing functional variation wild populations development laboratory strains. Advances zooarchaeology population genomics will usher new golden age research on biology rats, positive feedbacks use as biomedical models.

Language: Английский

---

The genomic response to urbanization in the damselfly Ischnura elegans

Evolutionary Applications, Journal Year: 2023, Volume and Issue: 16(11), P. 1805 - 1818

Published: Oct. 11, 2023

Abstract The complex and rapid environmental changes brought about by urbanization pose significant challenges to organisms. multifaceted effects of often make it difficult define pinpoint the very nature adaptive urban phenotypes. In such situations, scanning genomes for regions differentiated between non‐urban populations may be an attractive approach. Here, we investigated genomic signatures adaptation in damselfly Ischnura elegans sampled from 31 rural localities three geographic regions: southern northern Poland, Sweden. Genome‐wide variation was assessed using more than 370,000 single nucleotide polymorphisms (SNPs) genotyped ddRADseq. Associations SNPs level were tested two genetic environment association methods: Latent Factors Mixed Models BayPass. While found numerous candidate a highly overlap candidates identified methods within regions, there distinctive lack repeatability both at individual regions. However, “synapse organization” top functional categories enriched among genes located proximity SNPs. Interestingly, overall significance built up accretion different associated with This finding is consistent polygenic adaptation, where response achieved through subtle adjustment allele frequencies that contribute Taken together, our results point nervous system, specifically implicating involved synapse organization, which mirrors findings several behavioral studies other taxa.

Language: Английский

---

Urban rendezvous along the seashore: Ports as Darwinian field labs for studying marine evolution in the Anthropocene

Evolutionary Applications, Journal Year: 2022, Volume and Issue: 16(2), P. 560 - 579

Published: July 2, 2022

Humans have built ports on all the coasts of world, allowing people to travel, exploit sea, and develop trade. The proliferation these artificial habitats associated maritime traffic is not predicted fade in coming decades. Ports share common characteristics: Species find themselves novel singular environments, with particular abiotic properties-e.g., pollutants, shading, protection from wave action-within communities a melting pot invasive native taxa. Here, we discuss how this drives evolution, including setting up new connectivity hubs gateways, adaptive responses exposure chemicals or biotic communities, hybridization between lineages that would never come into contact naturally. There are still important knowledge gaps, however, such as lack experimental tests distinguish adaptation acclimation processes, studies understand putative threats port natural populations better outcomes fitness effects anthropogenic hybridization. We thus call for further research examining "biological portuarization," defined repeated evolution marine species ecosystems under human-altered selective pressures. Furthermore, argue act giant mesocosms often isolated open sea by seawalls locks so provide replicated life-size evolutionary experiments essential support predictive sciences.

Language: Английский

---

Ancient origin of an urban underground mosquito

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

Published: Jan. 28, 2025

Abstract Understanding how life is adapting to urban environments represents an important challenge in evolutionary biology. Here we investigate a widely cited example of adaptation, Culex pipiens form molestus , also known as the London Underground Mosquito. Population genomic analysis ∼350 contemporary and historical samples counter popular hypothesis that originated belowground less than 200 years ago. Instead, show first adapted human aboveground Middle East over course >1000 years, likely concert with rise agricultural civilizations. Our results highlight role early society priming taxa for evolution have implications understanding arbovirus transmission.

Language: Английский

---