Understanding how different ecological types within a species are formed and sustained is a key question in evolutionary biology. We examine this question through comprehensive resequencing of the genomes in a species of toad-headed agama (Phrynocephalus putjatai) endemic to the northeastern Qinghai-Tibetan Plateau, which exhibits considerable adaptive variation across three distinct habitats: desert, semi-desert, and meadow. We revealed the differentiation of these ecotypes started ~10,000 years ago and identified varying degrees of gene flow among them. The desert and meadow ecotypes originated from the semi-desert ecotype, and subsequently underwent directional selection in two contrasting habitats of desert and meadow. By analyzing the genomic basis of ecotype differentiation, we identified a single ~170-kb locus encompassing two tightly linked MYH genes, which may play a major role in facilitating the rapid adaptation to desert and meadow habitat in P. putjatai. This locus is likely to have experienced recent strong positive selection in both desert and meadow ecotypes and originated prior to their divergence. Our findings provide compelling evidence that the P. putjatai ecotypes recently diverged from a common source, and local adaptation to different habitats involves the sorting of ancestral genetic variation. This study underscores how selection acting on ancestral standing genetic variation can drive rapid local adaptation and diversification despite gene flow.

Most amniote genomes are diploid, moderate in size (approximately 1–6 g), and contain a large proportion of repetitive sequences. The development of next-generation sequencing technology has made it possible to resolve the genome assembly of non-model species. However, traditional genome assembly methods usually involve the acquisition of a large amount of sequencing data and complex calculations, making the de novo genome for non-model species expensive and difficult for most projects. The development of long-read sequencing, especially the emergence of high-fidelity (HiFi) long-read data, has made it possible to assemble genomes efficiently, but how to obtain high-quality reference genomes economically and quickly still lacks practical evaluation. Here we de novo assembled the first chameleon genome, the panther chameleon (Furcifer pardalis). We obtained chromosome-level contigs using only HiFi data, and further combined Hi-C data to assemble all contigs to pseudochromosomes. We also found that sequencing depth > 30 folds can ensure both the integrity and accuracy of the genome, while insufficient depth led to false increase in genome size and proportion of duplicated genes. Our results provide an accurate and efficient de novo assembly strategy for reference genomes of non-model species.

Whether oviparous or viviparous species are more vulnerable to climate warming is a long-standing puzzle. In this study, we developed a novel life history model to quantify the impact of climate change on maternal energy budget and offspring survival of squamate species with either parity mode. We demonstrate that climate warming will increase energy intake by adults without affecting reproductive success and increase offspring survival in viviparous species. In contrast, climate warming will induce a significantly increased reproductive output in oviparous species, which exceeds the energy intake by adults. In particular, in most subtropical regions, warming may cause oviparous females to produce more offspring with reduced survival, leading to low reproductive efficiency. These results suggest that oviparous squamates may be more vulnerable to climate warming than viviparous species in the broad sympatric zone of these species.