Genome-wide parallelism underlies contemporary adaptation in urban lizards

Abstract

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

Keywords: Anolis; parallelism; rapid adaptation; urban evolution; urbanization.

Fig. 1.

Environmental and population divergence. We sampled paired urban–forest sites in three municipalities (regions) across the island of Puerto Rico. Population structure analyses support independent urban–forest pairs in each geographic region. Across all panels, colors correspond to municipality and site, as follows: Arecibo, urban: pink, forest: purple; Mayagüez, urban: light blue, forest: dark blue; San Juan: urban: orange, forest: red. (A) Satellite imagery of forest and urban sites sampled in each municipality (images: Google Earth and Maxar Technologies 2001). Estimated dates of urban establishment are indicated below the urban images. (B) Urban and forest habitats differ in parallel in multidimensional habitat space, with urban environments characterized by substantially reduced tree cover, extensive impervious surface cover, warmer and drier climate, artificial light at night, and abundant anthropogenic structures. Principal components analysis of habitat indicates parallel shifts across the three municipalities in multivariate habitat space between urban and forest sites. (C) DAPC of genomic variation overlaid on a map of Puerto Rico showing urbanization extent (23) in black. Individual samples are colored by site. Gray triangles indicate geographic locations of municipalities sampled. (D) Midpoint-rooted sample tree, with individual samples colored by site. Individuals from within each region (but not necessarily each habitat type within region) were more genetically similar to one another on average than to individuals from other regions.

Fig. 2.

Parallelism of urban-associated genomic changes. (A) Manhattan plot of SNPs identified by the urban genotype–environment association test (GEA), with the significance threshold indicated by the black dotted line and genes containing shared outlier SNPs listed next to the peaks for chromosomes 2 and 4. We complemented this analysis with three PCAs, one for each municipality: (B) Arecibo, (C) Mayagüez, and (D) San Juan. Colored points in each Manhattan plot are the 91 SNPs identified in all four tests, and all outlier SNPs are shown in B–D in gray. (E) The peak on chromosome 1 identified by the blue rectangle is shown in greater detail with genes containing shared outlier SNPs across the GEA and PCA analyses listed. (F) Venn diagram of overlap in genes containing outlier SNPs across the three municipalities in the PCA analyses and the GEA. The 33 urban-associated genes contained outlier SNPs in all four tests. Larger versions of all Manhattan plots are in SI Appendix, Fig. S5.

Fig. 3.

Phenotypic parallelism and genomic underpinnings. We focused on six morphological traits with known urban-associated divergence: (A) forelimb and hindlimb lengths, (B) front toepad area, (C) front toepad lamella count, (D) rear toepad area, (E) rear toepad lamella count. (F) At the phenotypic level: mean and SE for each trait across all populations by habitat type (urban, forest) with individuals colored by municipality: pink, Arecibo; blue, Mayagüez; red, San Juan, with mean and SE by habitat shown in black. At the genomic level: overlap in outlier SNPs for each of the three traits between posterior (blue points) and anterior elements (green points) for each trait: (G) limbs, (H) toepad area, and (I) toepad lamellae; SNPs associated with both hindlimb and forelimb elements are indicated in the upper right quadrant (teal points). Outlier SNPs associated with urbanization (GEA analysis) are shown as hollow gray diamonds, with filled red diamonds indicating urban SNPs that also overlap with both forelimb and hindlimb morphological elements. Gene names correspond to one or more of the urban-morphology SNPs in the upper right quadrant (red diamond).

Fig. 4.

Parallelism of genomic architecture of urban morphology. We performed local PCAs of outlier SNPs for each of the six morphological traits. The first axis of genomic variation summarized by each PCA (eigenvector 1) indicates parallel genomic change in the urban–forest pairs across the three municipalities for (A), forelimb length (FL) and hindlimb length (HL); (B) front lamellae (FLAM) and rear lamellae (RLAM), (C) front toepad area (FTP) and rear toepad area (RTP). In each plot A–C colored points indicate individuals colored by population, and black/white points indicate the mean and SE across all population pairs. We also examined allele-level divergence across the three urban–forest pairs, summarized by the effect sizes (partial eta, η²) of habitat and the interaction of habitat by municipality, where a greater effect size of habitat versus the interaction effect (points above the black 1:1 dashed line) indicates a parallel response associated with urbanization, whereas a greater interaction effect (points below the black dashed line) indicate municipality specific, idiosyncratic divergence between urban and forest populations (e.g., local adaptation). Front (filled points) and rear (hollow points) elements for each trait are shown in each plot for (D) limb length, (E) lamellae, and (F) toepad area. (G) The mean and SE of the difference between the habitat and interaction effect sizes for each trait is compared to the null expectation (mean effect size of background SNPs; red dashed line). As in D–F the black dotted line indicates equal effect size of habitat (urban) and municipality specific divergence. Significance levels by the two-sided t test against the null expectation: P = 0.01**, P < 0.001***.