Rosa Rubicondior: Unintelligent Design - Stupidly Doing The Same Thing In Two Different Ways

Monday, 21 April 2025

Unintelligent Design - Stupidly Doing The Same Thing In Two Different Ways

Timema cristinae (striped morph)

Credit: Bart Zijlstra www.bartzijlstra.com

USU Evolutionary Biologist Says Study Reveals Complex Chromosomal Rearrangements in a Stick Insect

The wingless, plant-feeding stick insect, Timema cristinae, occurs in two different cryptic colour morphs. One has longitudinal white stripes along its back on an otherwise green body, while the second is a uniform plain green.

The striped morph is found on Adenostoma fasciculatum, a plant with long, needle-like leaves, where the stripes help break up the outline of the insect’s body, making it resemble a cluster of green needles. In contrast, the plain green morph is found on Ceanothus spinosus, which has broader, more tree-like leaves on which conspicuous white stripes would be maladaptive.

This seems entirely sensible and, from the perspective of an intelligent designer, a perfectly reasonable way to protect stick insects from predation — setting aside, for the sake of argument, the questionable logic of designing predators to eat stick insects and then designing stick insects to avoid being eaten.

However, the means by which this cryptic colouration was achieved in populations of Timema cristinae on two different mountains, where the respective host plants grow, is more typical of the behaviour of creationism’s putative designer. In each case, the same camouflage was achieved through entirely different genetic mechanisms. This tendency to reinvent the metaphorical wheel appears to be a hallmark of creationism’s “intelligent” designer — seen, for example, in the development of different wing structures in birds and bats, different forms of insulation in mammalian fur and bird feathers, and several distinct designs for eyes.

Of course, there is no reason to expect a mindless natural process such as evolution by natural selection to respond to identical environmental pressures in precisely the same way in two geographically isolated populations. All that matters is whether the eventual adaptation — in this case, effective camouflage — is functionally comparable.

What information do you have on the evolution, distribution and life cycle of stick insects? Stick Insects: Evolution, Distribution, and Life Cycle

Evolutionary Background
Stick insects (order Phasmatodea) are an ancient group of herbivorous insects that have evolved a range of sophisticated camouflage strategies to avoid predation, including mimicry of sticks, leaves, and even moss or bark. Fossils dating back to the Early Eocene (~56 million years ago) show that stick insects have been employing these strategies for tens of millions of years. Molecular phylogenetics suggests that stick insects may be even older, possibly originating in the Cretaceous (~100 million years ago).

Their evolution includes repeated, independent gains and losses of wings and transitions between flightless and flying forms. The evolution of parthenogenesis (asexual reproduction) in many species also reflects their adaptability to isolated or low-density habitats.

Evolutionary Relationships
Stick insects (Phasmatodea) are part of the larger insect superorder Polyneoptera, which also includes grasshoppers (Orthoptera), earwigs (Dermaptera), and cockroaches and termites (Blattodea). Among these, they are most closely related to cockroaches and mantids (Mantodea), with whom they share certain structural and genetic traits.

Recent molecular studies suggest that Phasmatodea and Mantodea may form a clade known as Eukinolabia, characterised by adaptations in the mouthparts and development. Despite their slow, herbivorous lifestyle, stick insects are thus part of a lineage that includes some of the insect world’s most formidable predators.

This evolutionary relationship is especially interesting in light of their very different ecological roles—while mantids are fast-moving ambush predators, stick insects are masters of crypsis and specialised herbivores. Their divergence likely reflects ancient adaptive specialisation to different ecological niches.

Global Distribution
Stick insects are found on all continents except Antarctica, with the highest diversity in tropical and subtropical regions such as Southeast Asia, Australia, Central and South America. Some temperate species occur in North America and parts of Europe, including the UK (Bacillus rossius and Clonopsis gallica introduced in southern regions).

Their success in many regions is closely tied to their cryptic morphology, which reduces predation and allows them to occupy a wide range of vegetation types. Many species are highly host-specific, evolving to mimic the specific plants on which they feed.

Life Cycle
Stick insects undergo incomplete metamorphosis (hemimetabolism), meaning they hatch from eggs into nymphs that resemble miniature, wingless adults. They then go through several moults (instars), gradually increasing in size and, in some species, developing wings.

Key features of the stick insect life cycle:

Eggs: Often resemble seeds and can take weeks to months to hatch. Some species even flick their eggs onto the ground where they blend into leaf litter.
Parthenogenesis: Many species can reproduce without mating. In these cases, females produce genetic clones of themselves, enabling population persistence in the absence of males.
Nymph Stage: Juvenile stick insects mimic twigs or leaves and may even sway like a plant in the wind to enhance their disguise.
Adults: Some species remain wingless throughout life, while others (especially in tropical regions) develop wings for gliding or short bursts of flight.

Stick insects are mostly nocturnal, feeding at night on leaves. Their slow, deliberate movements, coupled with impressive camouflage, make them difficult for predators to detect.

Indeed, this appears to be exactly what occurred with these stick insects, as recently discovered by a team of biologists from Utah State University (USU), led by Professor Zachariah Gompert. Their findings, published in Science, show that cryptic colouration evolved via two distinct and complex chromosomal rearrangements. In each population, millions of DNA base pairs were inverted and relocated from one region of the genome to another — independently. One rearrangement involved 299 genes; the other, just 97.

USU Evolutionary Biologist Says Study Reveals Complex Chromosomal Rearrangements in a Stick Insect
In the April 17 online issue of the AAAS journal Science, Zachariah "Zach" Gompert and colleagues use multiple phased genome assemblies and population-level DNA sequencing data to show complex chromosomal rearrangements are key drivers of repeated adaptive evolution in a stick insect.
Understanding the material basis of adaptive evolution has been a central goal in biology dating back to at least the time of Darwin. One focus of current debates is whether adaptive evolution relies on many mutations with small and roughly equal effects or if it is driven by one or a few mutations that cause major changes in traits.

Utah State University evolutionary biologist Zachariah Gompert says chromosomal rearrangements where large chunks of chromosomes are inverted, moved, deleted or duplicated provide a possible source for such large-scale “macromutations.” However, characterizing chromosomal rearrangements with common DNA sequencing methods has been difficult.

He says many organisms, including humans are diploid, meaning they have two sets of chromosomes — one from each parent. The same is true for stick insects. This makes identifying chromosomal rearrangements with species challenging when assembling genomes.

In the past, we’ve averaged data from each chromosome set, but the limited accuracy of this method doesn’t tell the whole story. Using newer, molecular and computational approaches that generate phased genome assemblies where the two copies of each chromosome are assembled separately, has enabled us to directly show how complex chromosomal rearrangements have allowed stick insects to adapt by being cryptic on different host plants and thereby avoid predation.

Professor Zachariah Gompert, lead author
Department of Biology and the USU Ecology Center
Utah State University, UT, USA.

In the April 17 online issue of the American Association for the Advancement of Science journal Science, Gompert and colleagues report adaptive divergence in cryptic color pattern is underlain by two distinct, complex chromosomal rearrangements, where millions of bases of DNA were flipped backwards and moved from one part of a chromosome to another, independently in populations of stick insects on different mountains.

Contributing authors on the paper include Gompert’s longtime collaborator Patrik Nosil and other researchers from the French National Center for Scientific Research, along with scientists from the University of Notre Dame, the University of Nevada, Reno, and The Institute of Cancer Research in the United Kingdom. The research is supported by the National Science Foundation and the European Research Council.

The scientists studied Timema cristinae insects with varied color patterns, collected from two mountains near Santa Barbara, California. The wingless, plant-feeding insects are divergently adapted to two different plant species in the coastal chaparral habitats. One stick insect pattern is green, allowing it to blend in with the California lilac, while the other sports a thin, white stripe on its back making it nearly undetectable among the needle-like leaves of the chamise shrub.

Gompert and colleagues showed that this adaptive difference in color pattern is almost completely explained by the presence versus absence of these individual complex, chromosomal rearrangements.

The new phased genomic assembly technology used in this study was a critical piece in helping us examine how color pattern evolved in these insects. Our findings suggest chromosomal rearrangements might be more widespread and more complex than we previously thought.

Professor Zachariah Gompert.

[Professor Gompert] says these mutations, despite being large, are easy to miss using traditional DNA sequencing approaches.

Chromosomal rearrangements can be difficult to detect and characterize using standard approaches. We’re essentially exploring the ‘dark matter’ of the genome. We’re just scratching the surface. We’ve lacked the tools to detect structural variation, but with improved technology we hypothesize it plays a more important role in evolution than previously recognized.

Professor Zachariah Gompert.

Structural variation, he says, rather than being rare, may be regularly available to prompt evolution.

Structured Abstract

INTRODUCTION
The fit of organisms to their environment is a hallmark of adaptive evolution and can lead to the emergence of new species and thus create biological diversity. Therefore, understanding the genetic basis of local adaptation remains a major goal in biology. Structural genetic elements such as chromosomal inversions, insertions, deletions, and translocations are widespread across genomes and have increasingly been shown to shape evolution. However, the complexity of such elements and their role in repeatedly driving local adaptation remain unclear. Comparisons of haplotype-resolved or phased genome assemblies from multiple individuals provide new opportunities to understand how structural variation contributes to evolution, particularly in regard to the repeatability of evolution.

RATIONALE
Timema cristinae is a wingless, plant-feeding stick insect that exhibits two color-pattern morphs that are divergently adapted to two different plant species. On the plant Adenostoma fasciculatum, one often finds a striped color-pattern morph of T. cristinae that is green but also bears a longitudinal, white stripe on its dorsal surface. Past work has shown that this morph is cryptic on the thin needle-like leaves of A. fasciculatum. On an alternative host, the larger and more tree-like Ceanothus spinosus, one often finds an unstriped morph that is green but lacks the dorsal stripe, making it cryptic against the broad leaves of C. spinosus. Thus, the color-pattern morphs are adaptations to different hosts that promote camouflage and survival in the face of visual predation by birds and lizards. Both these morphs are found on two different mountains (Refugio and Highway 154) near Santa Barbara, California. In this work, we leveraged phased genome assemblies of each morph from each mountain to dissect the genetic basis of color-pattern polymorphism. We coupled these genomes with population genetics data to infer the evolutionary history of the morphs and the roles of selection, present gene flow, and historical introgression in their origin and maintenance.

RESULTS
Phased genome assemblies show that adaptive divergence in cryptic color pattern is repeatedly underlain by structural variation, but not a simple chromosomal inversion. We found that color pattern in populations on two different mountains is associated with translocations that have also been inverted. These complex structural variants span ~43 and ~15 mega–base pairs on the two mountains and contain 299 and 97 genes, respectively. The translocations arose independently on each mountain, representing repeated evolution. Although the translocations differ in size and origin on each mountain, they overlap partially such that the inverted region and a small segment of the colinear region of the translocation on one mountain coincide with the colinear region of the translocation on the other mountain. Consequently, these structural variants contain some of the same gene regions, including candidate color-pattern genes. We also provide evidence that this structural variation is subject to divergent selection along a geographic cline and arose without introgression between species. The results thus show how the origin of complex structural variation provides a mechanism for repeated bouts of adaptation.

CONCLUSION
We report structural variation underlying an adaptive polymorphism in a stick insect. Related results reported in other plants and animals point to a general role for structural variation in adaptive evolution. However, we show here that such structural variation can be complex and diverse, not always representing a simple chromosomal inversion, with differences among populations of a single species. Structural variation may be regularly available as a substrate for evolution, yet its importance may be presently underestimated because scientists have lacked powerful tools to detect it. Thus, accumulating examples of inversions and supergenes may only be the beginning. Indeed, our findings suggest that structural variation could be an abundant, diverse, and widespread source of genetic variation, providing fuel for evolution. Moreover, such variation may arise repeatedly to provide an element of predictability to adaptive evolution. Ongoing advances in genomics will allow this idea to be tested in a wide range of organisms and contexts.

Adaptive divergence in cryptic color pattern in T. cristinae stick insects is repeatedly underlain by complex structural variation.
T. cristinae exhibits two color-pattern morphs—striped and green—that are divergently adapted to two different plant species. Color pattern in populations of these stick insects on each of two different mountains is associated with large translocations that have also been inverted. These translocations differ in size and origin on each mountain, but they overlap partially and are associated with some of the same genes. mya, million years ago; Ne, effective population size; Nm, number of migrants per generation.

Abstract
Structural elements are widespread across genomes, but their complexity and role in repeatedly driving local adaptation remain unclear. In this work, we use phased genome assemblies to show that adaptive divergence in cryptic color pattern in a stick insect is repeatedly underlain by structural variation, but not a simple chromosomal inversion. We found that color pattern in populations of stick insects on two mountains is associated with translocations that have also been inverted. These translocations differ in size and origin on each mountain, but they overlap partially and involve some of the same gene regions. Moreover, this structural variation is subject to divergent selection and arose without introgression between species. Our results show how the origin of structural variation provides a mechanism for repeated bouts of adaptation.

Zachariah Gompert et al.
Adaptation repeatedly uses complex structural genomic variation. Science 388, eadp3745 (2025). DOI:10.1126/science.adp3745

© 2025 American Association for the Advancement of Science.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

Perhaps William A. Dembski of the Discovery Institute — who asserts that such genetic information is “complex and specified” and could only be produced by an intelligent designer — can explain why a designer would choose to provide “complex specified information” in two entirely different forms to achieve the same result. Moreover, if such specificity can be achieved in multiple, unrelated ways, how are we to distinguish it from information that is not “complex” or “specified” at all?

The other point for Discovery Institute and other CDesign Proponentsists to explain is why, if biologists are turning their backs on 'Darwinism' in favour of evidence-free supernatural creationism, these biologists show no evidence of that interpretation of these findings. Instead of settling for the simplistic, unscientific 'God did it!' answer of ID creationism, they seek to explain this divergence in terms of the evolutionary mechanism of mutation and natural selection.

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