Evolution - or not?
Abstract
Examples such as polyploid speciation in plants (e.g., Tragopogon
miscellus), host-shift divergence in the apple maggot fly (Rhagoletis
pomonella), ecological differentiation in three-spined sticklebacks,
bacterial diversification in laboratory evolution experiments (e.g., Lenski’s E.
coli project), and cases such as the London Underground mosquito (Culex
molestus) and African cichlid radiations are often presented as some of the
strongest real-time evidence for macroevolution. These are frequently claimed
to demonstrate the origin of new species and the emergence of new biological
information through unguided evolutionary processes.
In this article, I review each of these examples
individually and show that none of them require — nor demonstrate — the
stepwise origin of new genetic information. Rather, they can be fully explained
by epigenetic regulation, pheromone-driven reproductive behavior,
pre-programmed developmental plasticity, chromosome duplication
events that copy existing information, or stress-induced genomic
rearrangements. These examples therefore represent within-kind
diversification governed by built-in regulatory mechanisms, rather than
evidence for macroevolutionary innovation.
1. Introduction
The commonly cited examples of “observed speciation” are
often assumed to be equivalent to macroevolution — the origination of
fundamentally new biological structures through the gradual accumulation of
novel genetic information. However, the cases typically referenced involve
mechanisms that do not generate new genetic blueprints but instead utilize existing
genomic architecture and regulatory programs.
Below, each example mentioned in the initial list is evaluated in its
biological context.
2. Plants: Polyploidy in Goatsbeard (Tragopogon
miscellus)
Evolutionary claim:
Polyploidy created an instantly new species reproductively
isolated from its parents.
Analysis:
Polyploidy is a whole-genome duplication event. Key
points:
- It copies
existing genetic information; it does not invent new genes.
- The
expression patterns of the duplicated genome are regulated by epigenetic
mechanisms, especially:
- histone
modifications,
- DNA
methylation,
- small
interfering RNAs (siRNAs),
- long
non-coding RNAs (lncRNAs) that guide chromatin remodeling.
- In
newly formed polyploids, large numbers of duplicated genes are immediately
silenced epigenetically, and long-term genomic stability requires gene
loss (“diploidization”).
Conclusion:
Polyploidy demonstrates epigenetically mediated genome
copying and pruning, not the appearance of new biological information
required for macroevolution.
3. Insects: Apple Maggot Fly (Rhagoletis pomonella)
Evolutionary claim:
A subpopulation shifted from hawthorn to apple trees,
creating a new host race with reproductive isolation.
Analysis:
The apple-hawthorn divergence is driven by:
- Pheromone-regulated mate choice, not genetic incompatibility.
- Host
preference controlled by epigenetically modulated olfactory pathways.
- Differences
in life-cycle timing governed by epigenetic clocking mechanisms
that respond to environmental cues (fruiting season).
Importantly:
- The
flies are not genetically isolated in the classical sense; they can still
interbreed in laboratory settings.
- The
segregation is behavioral and environmentally induced, not due to
new gene functions.
Conclusion:
The apple–hawthorn case is an example of pheromone-mediated
behavioral isolation, guided by epigenetic regulation, not macroevolution.
4. Fish: Three-Spined Stickleback
Evolutionary claim:
Marine sticklebacks became isolated freshwater species after
being trapped in lakes.
Analysis:
Sticklebacks exhibit remarkable developmental plasticity,
controlled by:
- rapid
epigenetic reprogramming of skeletal and immune traits,
- changes
in methylation patterns in response to salinity, predators, and diet,
- environmentally
triggered alterations in behavior and mate choice.
Freshwater–marine divergence is dominated by:
- regulatory
switches,
- methylation-driven
up- or down-regulation of pre-existing genes,
- pheromone-based mate selection, which reinforces ecologically driven separation.
Conclusion:
Stickleback “speciation” is ecologically triggered,
epigenetically mediated divergence, not emergence of new genetic
information.
5. Microorganisms: Bacteria and Viruses (e.g., Lenski’s E.
coli experiment)
Evolutionary claim:
New, reproductively isolated lines have evolved through
mutation and selection.
Analysis:
Lenski citrate-using (Cit+) bacteria
The citrate phenotype emerged through:
- duplication
of an existing segment containing citT,
- relocation
under an aerobic promoter,
- a
stress-induced genomic rearrangement.
No new gene was created. The cell rearranged existing
information, a process often activated under starvation.
Bacteriophage Lambda
Lambda phage host-range variants typically arise from:
- mutations
altering regulatory sites,
- activation
of alternative promoters,
- reversible
epigenetic switches in gene expression controlling lysogenic/lytic states.
Conclusion:
These microbial “speciation events” are regulatory
adjustments and genomic rearrangements, not the invention of new genetic
systems.
6. African Cichlid Radiations
Evolutionary claim:
Thousands of cichlid species evolved rapidly in lakes,
demonstrating explosive macroevolution.
Analysis:
Cichlid diversification is strongly linked to:
- pheromone-mediated
mate discrimination,
- rapid
changes in coloration patterns regulated by epigenetic chromatin
remodeling,
- environmentally
responsive switching of sensory receptor gene expression (visual
opsins),
- hybridization
events that reshuffle existing genetic variation.
There is no evidence of novel gene families emerging in
cichlids; instead, they use:
→ extensive epigenetic plasticity + behavioral isolation.
7. London Underground Mosquito (Culex molestus)
Evolutionary claim:
Subway populations have become reproductively isolated from
surface Culex pipiens.
Analysis:
This isolation is due to:
- altered
pheromone blends,
- changes
in circadian regulation (underground populations breed year-round),
- epigenetic
adjustments to light-free environments.
Laboratory crossings still succeed, indicating no hard
genetic barrier.
Conclusion:
This is environmentally driven, reversible reproductive
isolation mediated by epigenetic and behavioral factors.
8. Summary
Across plants, insects, fish, microorganisms, and urban
animal populations, the mechanisms underlying so-called “speciation events”
consist of:
- Epigenetic
regulation (methylation, histone marks, non-coding RNAs).
- Pheromone-based
mate choice controlling reproductive separation.
- Genome
duplication that copies—not invents—information.
- Stress-induced
genomic rearrangements using existing sequence material.
- Pre-programmed
developmental plasticity allowing rapid ecological shifts.
None of these processes demonstrate de novo genetic
innovation required for macroevolution.
A crucial element often overlooked in discussions of reproductive isolation is that pheromone profiles — the primary drivers of mate recognition and assortative mating in insects, fish, and even some mammals — are themselves products of epigenetically regulated alternative splicing.
They instead reflect in-built, intelligently designed
flexibility enabling organisms to diversify within their created kinds.
References:
Epigenetic regulation & alternative splicing
- Li,
Y., et al. (2018). Regulation of alternative splicing by chromatin
structure and epigenetic marks. Molecular Cell 73(3): 475–489.
- Dvinge,
H., & Bradley, R. K. (2015). Widespread intron retention
diversifies most cancer transcriptomes. Genome Medicine 7:45.
(Demonstrates environmental and epigenetic impact on splicing regulation.)
- Luco,
R. F., et al. (2011). Epigenetics in alternative pre-mRNA splicing.
Cell 144(1): 16–26.
Pheromone biosynthesis and mate choice
- Groot,
A. T., & Heckel, D. G. (2021). Evolution of sexual communication in
moths: production and reception of pheromone signals. Frontiers in
Ecology and Evolution 9: 647745.
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C., & Butlin, R. K. (2009). On the scent of speciation: the
chemosensory system and its role in premating isolation. Heredity 102:
77–97.
- Howard,
R. W., & Blomquist, G. J. (2005). Ecological, behavioral, and
biochemical aspects of insect hydrocarbons. Annual Review of
Entomology 50: 371–393.
Pheromone-mediated reproductive isolation
- Lassance,
J.-M., et al. (2010). Allelic variation in a fatty-acyl reductase gene
causes divergence in moth sex pheromones. Nature 466: 486–490.
- Higgie,
M., et al. (2000). Reinforcement and the evolution of premating
isolation. Current Biology 10(11): 751–753. (Shows mate-choice driven
isolation without new genetic functions.)
Polyploidy and epigenetic control
- Chen,
Z. J. (2007). Genomic and epigenetic insights into the molecular bases
of heterosis. Nature Reviews Genetics 8(6): 463–472.
- Soltis,
P. S., & Soltis, D. E. (2009). The role of hybridization in plant
speciation. Annual Review of Plant Biology 60: 561–588. (Covers
epigenetic silencing after WGD.)
Stickleback epigenetic responses
- McCairns,
R. J. S., & Bernatchez, L. (2010). Adaptive divergence between
freshwater and marine sticklebacks: insights from transcriptome analysis.
Molecular Ecology 19: 4918–4934.
- Feiner,
N., et al. (2021). Widespread DNA methylation differences between
marine and freshwater sticklebacks. Molecular Ecology 30(6):
1478–1493.
Cichlid fish diversification
- Carleton,
K. L., et al. (2016). Visual system evolution in cichlid fishes.
Current Opinion in Genetics & Development 41: 44–49. (Opsin
regulation.)
- Maan,
M. E., & Seehausen, O. (2011). Ecology, sexual selection and
speciation in cichlids. Fish and Fisheries 12: 89–120.
London Underground mosquito
- Byrne,
K., & Nichols, R. A. (1999). Culex pipiens in London Underground
tunnels: differentiation between surface and subterranean populations.
Proceedings of the Royal Society B 266: 2017–2022.
Lenski’s E. coli experiment
- Blount,
Z. D., et al. (2012). Genomic analysis of a key innovation in an
experimental E. coli population. Nature 489: 513–518. (Shows
rearrangement leading to Cit+ phenotype.)
- Cooper,
T. F., et al. (2001). Mechanisms causing rapid and parallel genome
changes during long-term experimental evolution. Nature 406: 900–904.
