F Rosa Rubicondior: Creationism in Crisis - Perto Rican Lizards Evolving

Sunday 15 January 2023

Creationism in Crisis - Perto Rican Lizards Evolving

Urban Lizards Share Genomic Markers Not Found in Forest-Dwellers
Puerto Rican crested anole, Anolis cristatellus
Puerto Rican crested anole, Anolis cristatellus
Photo credit: Kristin Winchell
Unlike creationism which, because it depends on magic and unproven, unfalsifiable magic supernatural entities, is incapable of making falsifiable predictions, the Theory of Evolution by Natural Selection (TOE) predicts that, from the same starting point, the same environmental changes will produce the same or very similar phenotypic changes, such as that recently reported for populations of lizards in Puerto Rico.

A paper recently published in Proceedings of the National Academy of Science (PNAS), reports on a case of parallel evolution between populations of the Puerto Rican crested anole, Anolis cristatellus, where unconnected populations in urban areas have evolved very similar adaptations to an urban environment compared to those living in a forest environment. The paper reports the findings of a team of researchers led by assistant professor of biology, Kristin Winchell, of New York University (NYU), NY, USA.

The NYU news release explains the research and its significance:
Studying Anolis cristatellus lizards in Puerto Rican cities and their surrounding forests, researchers find parallel physical differences and genomic signatures in urban populations

Lizards living in different cities have parallel genomic markers when compared to neighboring forest lizards, according to a new study published in the Proceedings of the National Academy of Sciences (PNAS).

The genetic variations linked to urbanization underlie physical differences in the urban lizards, including longer limbs and larger toe pads that show how these lizards have evolved to adapt to city environments.

Urbanization impacts roughly two-thirds of the Earth and is expected to continue to intensify, so it’s important to understand how organisms might be adapting to changing environments. In many ways, cities provide us with natural laboratories for studying adaptive change, as we can compare urban populations with their non-urban counterparts to see how they respond to similar stressors and pressures over short periods of time.

Assitant professor, Kristin Winchell, first author Department of Biology
New York University, New York, NY, USA.
Urbanization has dramatically transformed landscapes around the world—changing how animals interact with nature, creating “heat islands” with higher temperatures, and hurting local biodiversity. Yet many organisms survive and even thrive in these urban environments, taking advantage of new types of habitat created by humans. Researchers studying evolutionary changes in urban species have found that some populations, for example, undergo metabolic changes from new diets or develop an increased tolerance of heat.

Anolis cristatellus lizards—a small-bodied species also known as the Puerto Rican crested anole—are commonly found in both urban and forested areas of Puerto Rico. Prior studies by Winchell and her colleagues found that urban Anolis cristatellus have evolved certain traits to live in cities: they have larger toe pads with more specialized scales that allow them to cling to smooth surfaces like walls and glass, and have longer limbs that help them sprint across open areas.

Urban lizards had significantly longer limbs and larger toe pads with more specialized scales on their toes.
In the PNAS study, the researchers looked at 96 Anolis cristatellus lizards from three regions of Puerto Rico — San Juan, Arecibo, and Mayagüez—comparing lizards living in urban centers with those living in forests surrounding each city.

While we need further analysis of these genes to really know what this finding means, we do have evidence that urban lizards get injured more and have more parasites, so changes to immune function and wound healing would make sense. Similarly, urban anoles eat human food, so it is possible that they could be experiencing changes to their metabolism.

The physical differences we see in the urban lizards appear to be mirrored at the genomic level. If urban populations are evolving with parallel physical and genomic changes, we may even be able to predict how populations will respond to urbanization just by looking at genetic markers.

Understanding how animals adapt to urban environments can help us focus our conservation efforts on the species that need it the most, and even build urban environments in ways that maintain all species.

Assitant professor, Kristin Winchell
They first confirmed that the lizard populations in the three regions were genetically distinct from one another, so any similarities they found among lizards across the three cities could be attributed to urbanization. They then measured their toe pads and legs and found that urban lizards had significantly longer limbs and larger toe pads with more specialized scales on their toes, supporting their earlier research that these traits have evolved to enable urban lizards to thrive in cities.

To understand the genetic basis of these trait differences, the researchers conducted several genomic analyses on exomic DNA, the regions of the genome that code for proteins. They identified a set of 33 genes found in three regions of the lizard genome that were repeatedly associated with urbanization across populations, including genes related to immune function and metabolism.

In an additional analysis, they found 93 genes in the urban lizards that are important for limb and skin development, offering a genomic explanation for the increases in their legs and toe pads.

Do the differences in urban lizards apply to people living in cities? Not necessarily, according to Winchell, as humans aren’t at the whim of predators like lizards are. But humans are subject to some of the same urban factors, including pollution and higher temperatures, that seem to be contributing to adaptation in other species.
More technical detail is given by the scientists in the abstract to their paper in PNAS:

Urbanization drastically transforms landscapes worldwide, leading to altered eco-evolutionary dynamics. Many organisms are tolerant of, and even adapt to, these novel environments, presenting opportunities to study evolutionary change over rapid timescales. Here we provide a detailed investigation of the genomic basis of rapid adaptation in a species that thrives in urban environments. Integrating environmental, phenotypic, and genomic data, we demonstrate that populations exposed to similar environmental modification across distinct genetic clusters exhibit parallel phenotypic divergence underlain by parallel genomic divergence. We identify putative genomic targets of natural selection related to functionally relevant traits, thus helping to elucidate the mechanisms of rapid adaptive evolution of complex traits at the genomic level.


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.

Given that the environment acts to select for adaptive variations and against maladaptive ones, that this would happen as the anoles adopted an urban lifestyle is entirely predictable from the Theory of Evolution by natural selection. That these adaptations would be reflected in areas of the genome associated with those features, follows from our knowledge of both the genetic basis for the phenotype and of evolution. Unlike with Creationism, which must explain these parallel adaptations by reference to magic done by a putative but unproven supernatural designer, science has no need to invoke unproven, supernatural entities or magic because everything is explained by reference to natural processes.

And as goes almost without saying, there is no sign whatsoever that the TOE is inadequate to explain what can be observed as an example of evolution in progress and in just the relatively few years since large parts of Puerto Rica became urbanised.

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