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

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Climate change from an ectotherm perspective: evolutionary consequences and demographic change in amphibian and reptilian populations

Biodiversity and Conservation, Journal Year: 2024, Volume and Issue: 33(3), P. 905 - 927

Published: Feb. 14, 2024

Abstract Understanding how natural populations will respond to contemporary changes in climate is becoming increasingly urgent and of fundamental importance for the preservation future biodiversity. Among vertebrates, amphibians reptiles are more sensitive environmental perturbations than endotherms ectotherm diversity likely be disproportionally impacted by change. Notwithstanding concerns surrounding change resilience populations, accurately predicting population trajectories based on ecological physiological data alone remains challenging much can learnt studying have responded past. Genomic approaches now assay genetic at an unprecedented scale but date been relatively underutilised when demographic history reptiles. In this review, we first summarise changing climatic conditions may influence phenotype translate fitness dynamics. We then discuss relative role past shaping has traditionally approached a phylogeographic context expanding genomic resources species leveraged improve study demography many amphibian reptilian groups. An integrative approach that links known proximate effects due change, with ultimately enable us generate accurate models our ability assess

Language: Английский

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Sonic hedgehog and fibroblast growth factor 8 regulate the evolution of amniote facial proportions

Communications Biology, Journal Year: 2025, Volume and Issue: 8(1)

Published: Jan. 18, 2025

Language: Английский

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Piebaldism and chromatophore development in reptiles are linked to the tfec gene

Current Biology, Journal Year: 2023, Volume and Issue: 33(4), P. 755 - 763.e3

Published: Jan. 25, 2023

Language: Английский

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Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles

Animals, Journal Year: 2023, Volume and Issue: 13(3), P. 471 - 471

Published: Jan. 29, 2023

Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles—lizards and snakes—recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity phenotypic genomic traits, resources in non-avian have accumulated more slowly than they mammals birds, remaining amniotes. Here we review remarkable natural history reptiles, focus on physical characteristics, sequence compositional patterns that key axes variation across We argue high evolutionary can fuel new generation whole-genome phylogenomic analyses. A survey phylogenetic investigations shows capture-based approaches are commonly used, studies markers known ultraconserved elements (UCEs) especially well represented. However, many other types exist increasingly being mined from genome assemblies silico, including some greater information potential UCEs for certain investigations. discuss importance high-quality methods bioinformatically extracting range marker sets assemblies. Finally, encourage herpetologists working genomics, genetics, biology, fields to work collectively towards building squamates, rival those already place birds. Overall, development this cross-amniote tree life will contribute illuminate interesting dimensions biodiversity broader

Language: Английский

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On the causes, consequences, and avoidance of PCR duplicates: Towards a theory of library complexity

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: 23(6), P. 1299 - 1318

Published: April 16, 2023

Library preparation protocols for most sequencing technologies involve PCR amplification of the template DNA, which open possibility that a given DNA molecule is sequenced multiple times. Reads arising from this phenomenon, known as duplicates, inflate cost and can jeopardize reliability affected experiments. Despite pervasiveness artefact, our understanding its causes impact on downstream statistical analyses remains essentially empirical. Here, we develop general quantitative model distortions in data sets, leverage to investigate factors controlling occurrence duplicates. We show duplicate rate determined primarily by ratio between library complexity depth, noise (including dependence number cycles) only plays secondary role artefact. confirm predictions using new published RAD-seq libraries provide method estimate any set containing discuss how amplification-related artefacts analyses, particular genotyping accuracy. The proposed framework unites numerous observations made duplicates will be useful experimenters all where availability concern.

Language: Английский

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DNA methylation–based age prediction and sex-specific epigenetic aging in a lizard with female-biased longevity

Science Advances, Journal Year: 2025, Volume and Issue: 11(5)

Published: Jan. 31, 2025

Sex differences in life span are widespread across animal taxa, but their causes remain unresolved. Alterations to the epigenome hypothesized contribute vertebrate aging, and DNA methylation–based aging clocks allow for quantitative estimation of biological trajectories. Here, we investigate influence age, sex, interaction on genome-wide methylation patterns brown anole ( Anolis sagrei ), a lizard with pronounced female-biased survival longevity. We develop series age predictor models find that, contrary our predictions, rates epigenetic were not slower female lizards. However, states at loci acquiring age-associated changes appear be more “youthful” young females, suggesting that methylomes preemptively fortified early opposition direction age-related drift. Collectively, findings provide insights into reptiles suggest early-life profiles may informative than change predicting sex biases

Language: Английский

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Pre‐oviposition development of the brown anole (Anolis sagrei)

Developmental Dynamics, Journal Year: 2025, Volume and Issue: unknown

Published: April 17, 2025

The brown anole, Anolis sagrei, has emerged as a representative squamate species for developmental studies during the past decades. Novel functional tools have been established to manipulate embryogenesis through genome editing or introduction of small molecule inhibitors, and their effective use requires thorough understanding early anole embryogenesis. To enable precise reproducible staging embryos, we need knowledge progression morphogenesis. While post-oviposition development described, pre-oviposition period remains be explored. We provide first series anole. Analyzing follicles embryos brightfield imaging, SEM, STEM, histology, DAPI staining, define 26 distinct stages. Furthermore, followed heart development, neural crest cell migration, central nervous system using immunofluorescence analyses new comparative insights into morphogenesis each these organ systems. Our dataset reveals that peri-gastrulation up initiation neurulation diverges significantly from chick, common model reptile With this study, establish organism cross-clade evolutionary

Language: Английский

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The genetic basis of a colorful signal: the polymorphic dewlap of the slender anole (Anolis apletophallus)

Heredity, Journal Year: 2025, Volume and Issue: unknown

Published: April 30, 2025

Language: Английский

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Observing character displacement from process to pattern in a novel vertebrate community

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

Published: Nov. 14, 2024

Ecological character displacement, whereby shifts in resource use the presence of competing species leads to adaptive evolutionary divergence, is widely considered an important process community assembly and radiation. However, most evidence for displacement has been inferred from macro-scale geographic or phylogenetic patterns; direct tests underlying hypothesis divergent natural selection driving wild are rare. Here, we document between two ecologically similar lizards (Anolis sagrei A. cristatellus) experiencing novel contact. We identify directional during incipient stages sympatry a new that corresponds repeated trait divergence across multiple established sympatric communities. By identifying role as unfolds, connect how operating at short timescales may drive broader patterns distributions larger spatial temporal scales. When coexist, they often evolve differences reduce competition, called displacement. This study provides rare action, showing drives rapid changes when competitor arrives.

Language: Английский

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